# All installed under v3.6, and v4.2.2 with exception of mapproj, gdsfmt, SNPRelate
library(tidyverse); theme_set(theme_classic())
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## ✔ ggplot2   3.5.2     ✔ tibble    3.3.0
## ✔ lubridate 1.9.4     ✔ tidyr     1.3.1
## ✔ purrr     1.0.4     
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library(fs)
library(ggpubr)
library(ggbeeswarm)
library(gdsfmt)
library(SNPRelate)
## SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
library(ggrepel)
library(cowplot); theme_set(theme_cowplot(font_size=6))
## 
## Attaching package: 'cowplot'
## 
## The following object is masked from 'package:ggpubr':
## 
##     get_legend
## 
## The following object is masked from 'package:lubridate':
## 
##     stamp
# File paths for gasAcu5 masked aligned reads
ga5_roi_file <- "/labs/kingsley/ambenj/myosin_dups/analysis/ecotypic_depth/gasAcuv5_C4masked_nochrY/06_samtools_coverage_roi/roi_coverage_mapq3.txt"
metadata_file <- "/labs/kingsley/ambenj/myosin_dups/analysis/ecotypic_depth/metadata_227genomes.txt"
ga5_sim_roi_file <- "/labs/kingsley/ambenj/myosin_dups/analysis/ecotypic_depth/depth_simulations/206_genomes/02_coverage/stickleback_v5_assembly_MYH3C4dup_hardmasked_noChrY/roi_coverage_mapq3.txt"
# File paths for SNP data
#vcf_file_1 <- "/labs/kingsley/ambenj/myosin/ecotypic_depth_gasAcu1-4/227_genomes.final.filtered_chrXIX_2614822-2744076.vcf"
vcf_file_1 <- "/labs/kingsley/ambenj/myosin_dups/analysis/assemblies/gasAcu1-4/227_genomes.final.filtered.MYHSensitiveEcopeak.noDup.recode.vcf"
het_file <- "/labs/kingsley/ambenj/myosin_dups/analysis/assemblies/gasAcu1-4/227_genomes.final.filtered.MYHSensitiveEcopeak.noDup.het"
# Read roi file for gasAcu5 masked aligned reads
ga5_roi <- read_tsv(ga5_roi_file) %>% 
  mutate(bam = str_remove_all(bam, ".recal.realignGA5_C4masked.sort.merged.mkdup.bam|.recal.realignGA5_C4masked.sort.mkdup.bam|.recal.realignGA5_C4masked.sort.mkdup_mapq3_roi_coverage.txt|05_mkdup_index/"),
         type = "real") %>% 
  rename(samp = bam)
## Rows: 1816 Columns: 12
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (4): desc, region, chr, bam
## dbl (8): startpos, endpos, numreads, covbases, coverage, meandepth, meanbase...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ga5_roi
## # A tibble: 1,816 × 13
##    desc        region chr   startpos endpos numreads covbases coverage meandepth
##    <chr>       <chr>  <chr>    <dbl>  <dbl>    <dbl>    <dbl>    <dbl>     <dbl>
##  1 NLRC5       chrXI… chrX…  2601498 2.63e6     2206    28701     90.9      5.06
##  2 MYH3C1      chrXI… chrX…  2637324 2.65e6      835    11352     76.0      4.11
##  3 MYH3C2      chrXI… chrX…  2655758 2.67e6      558     9018     83.0      3.74
##  4 MYH3C3      chrXI… chrX…  2667295 2.68e6      567     8397     78.3      3.88
##  5 duplicatio… chrXI… chrX…  2665791 2.68e6      939    14097     80.0      3.91
##  6 SYT19       chrXI… chrX…  2697955 2.73e6     1383    21276     65.1      3.09
##  7 CALB2A      chrXI… chrX…  2745064 2.76e6     1193    14557     99.7      6.09
##  8 HTRA1A      chrVI… chrVI 14382418 1.44e7     1297    16460     96.1      5.65
##  9 NLRC5       chrXI… chrX…  2601498 2.63e6     2593    30765     97.5      6.18
## 10 MYH3C1      chrXI… chrX…  2637324 2.65e6     1042    13930     93.3      5.24
## # ℹ 1,806 more rows
## # ℹ 4 more variables: meanbaseq <dbl>, meanmapq <dbl>, samp <chr>, type <chr>
# Read simulations roi file for gasAcu5 masked aligned reads
ga5_sim_roi <- read_tsv(ga5_sim_roi_file) %>%
  mutate(bam = str_remove_all(bam, ".RG.sorted.bam|/labs/kingsley/ambenj/myosin_dups/analysis/ecotypic_depth/depth_simulations/206_genomes/01_alignment/stickleback_v5_assembly_MYH3C4dup_hardmasked_noChrY/"),
         type = "sim") %>%
  rename(samp = bam)
## Rows: 88 Columns: 12
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (4): desc, region, chr, bam
## dbl (8): startpos, endpos, numreads, covbases, coverage, meandepth, meanbase...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ga5_sim_roi
## # A tibble: 88 × 13
##    desc        region chr   startpos endpos numreads covbases coverage meandepth
##    <chr>       <chr>  <chr>    <dbl>  <dbl>    <dbl>    <dbl>    <dbl>     <dbl>
##  1 NLRC5       chrXI… chrX…  2601498 2.63e6     3042    28712     91.0      6.98
##  2 MYH3C1      chrXI… chrX…  2637324 2.65e6     1265    11214     75.1      6.21
##  3 MYH3C2      chrXI… chrX…  2655758 2.67e6      728     9274     85.3      4.96
##  4 MYH3C3      chrXI… chrX…  2667295 2.68e6      824     8341     77.8      5.70
##  5 duplicatio… chrXI… chrX…  2665791 2.68e6     1374    13856     78.6      5.77
##  6 SYT19       chrXI… chrX…  2697955 2.73e6     1740    17756     54.3      3.84
##  7 CALB2A      chrXI… chrX…  2745064 2.76e6     1515    14467     99.1      7.78
##  8 HTRA1A      chrVI… chrVI 14382418 1.44e7     1761    16829     98.2      7.74
##  9 NLRC5       chrXI… chrX…  2601498 2.63e6     3038    28434     90.1      6.94
## 10 MYH3C1      chrXI… chrX…  2637324 2.65e6     1074    11324     75.8      5.23
## # ℹ 78 more rows
## # ℹ 4 more variables: meanbaseq <dbl>, meanmapq <dbl>, samp <chr>, type <chr>
# Combine roi tables from real and sim samples
ga5_comb_roi <- rbind(ga5_roi, ga5_sim_roi)
ga5_comb_roi %>% 
  filter(type=="sim")
## # A tibble: 88 × 13
##    desc        region chr   startpos endpos numreads covbases coverage meandepth
##    <chr>       <chr>  <chr>    <dbl>  <dbl>    <dbl>    <dbl>    <dbl>     <dbl>
##  1 NLRC5       chrXI… chrX…  2601498 2.63e6     3042    28712     91.0      6.98
##  2 MYH3C1      chrXI… chrX…  2637324 2.65e6     1265    11214     75.1      6.21
##  3 MYH3C2      chrXI… chrX…  2655758 2.67e6      728     9274     85.3      4.96
##  4 MYH3C3      chrXI… chrX…  2667295 2.68e6      824     8341     77.8      5.70
##  5 duplicatio… chrXI… chrX…  2665791 2.68e6     1374    13856     78.6      5.77
##  6 SYT19       chrXI… chrX…  2697955 2.73e6     1740    17756     54.3      3.84
##  7 CALB2A      chrXI… chrX…  2745064 2.76e6     1515    14467     99.1      7.78
##  8 HTRA1A      chrVI… chrVI 14382418 1.44e7     1761    16829     98.2      7.74
##  9 NLRC5       chrXI… chrX…  2601498 2.63e6     3038    28434     90.1      6.94
## 10 MYH3C1      chrXI… chrX…  2637324 2.65e6     1074    11324     75.8      5.23
## # ℹ 78 more rows
## # ℹ 4 more variables: meanbaseq <dbl>, meanmapq <dbl>, samp <chr>, type <chr>
# Read whole genome files for gasAcu5 masked aligned reads
ga5_wg_files <- dir_ls(path = "/labs/kingsley/ambenj/myosin_dups/analysis/ecotypic_depth/gasAcuv5_C4masked_nochrY/06_samtools_coverage_wg/", glob = "*mapq3_wg_coverage.txt")
ga5_sim_wg_files <- dir_ls(path = "/labs/kingsley/ambenj/myosin_dups/analysis/ecotypic_depth/depth_simulations/206_genomes/02_coverage/stickleback_v5_assembly_MYH3C4dup_hardmasked_noChrY/", glob = "*mapq3_wg_coverage.txt")

# function to add file name to dataframe
read_and_record_filename <- function(filename){
  read_tsv(filename) %>%
  mutate(filename = path_file(filename))
  }

# gather real wg files into dataframe
ga5_wg <- map_df(ga5_wg_files, read_and_record_filename)%>% 
  mutate(samp = str_remove_all(filename, ".recal.realignGA5_C4masked.sort.merged.mkdup_mapq3_wg_coverage.txt|.recal.realignGA5_C4masked.sort.mkdup_mapq3_wg_coverage.txt|../ecotypic_depth/gasAcuv5_C4masked_nochrY/06_samtools_coverage_wg"))
ga5_wg
## # A tibble: 5,221 × 11
##    chr   startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq
##    <chr>    <dbl>  <dbl>    <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl>
##  1 chrI         1 2.96e7  2276751 28423668     96.0      5.74      27.2     57.8
##  2 chrII        1 2.37e7  1791949 22810471     96.3      5.65      27.2     58.7
##  3 chrI…        1 1.78e7  1368279 16754126     94.3      5.76      27.2     57.1
##  4 chrIV        1 3.42e7  2570661 32232528     94.3      5.60      27.2     57.8
##  5 chrIX        1 2.08e7  1640991 19485000     93.5      5.88      27.2     56.8
##  6 chrM         1 1.57e4    18096    14042     89.2     86.7       27.3     49.7
##  7 chrUn        1 1.99e7  1111456  9958942     50.1      4.12      27.2     36.7
##  8 chrV         1 1.56e7  1208332 14698641     94.5      5.80      27.1     57  
##  9 chrVI        1 1.88e7  1420598 17972608     95.5      5.64      27.2     58.5
## 10 chrV…        1 3.08e7  2322042 29052786     94.4      5.62      27.2     57.9
## # ℹ 5,211 more rows
## # ℹ 2 more variables: filename <chr>, samp <chr>
# Gather simualated wg files into dataframe
ga5_sim_wg <- map_df(ga5_sim_wg_files, read_and_record_filename)%>%
  mutate(samp = str_remove_all(filename, ".mapq3_wg_coverage.txt"))
ga5_sim_wg
## # A tibble: 253 × 11
##    chr   startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq
##    <chr>    <dbl>  <dbl>    <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl>
##  1 chrI         1 2.96e7  3010567 28374766     95.8      7.63      35.3     58.5
##  2 chrII        1 2.37e7  2424802 22882221     96.6      7.69      35.3     58.9
##  3 chrI…        1 1.78e7  1795109 16838045     94.8      7.59      35.3     58.3
##  4 chrIV        1 3.42e7  3454294 32344585     94.6      7.57      35.3     58.2
##  5 chrIX        1 2.08e7  2069660 19488540     93.5      7.45      35.3     58.2
##  6 chrM         1 1.57e4      756    10047     63.8      3.64      35.3     49.2
##  7 chrUn        1 1.99e7   711199  7345105     36.9      2.66      35.3     46.5
##  8 chrV         1 1.56e7  1579597 14729260     94.7      7.62      35.3     58  
##  9 chrVI        1 1.88e7  1905219 18005937     95.6      7.61      35.3     58.7
## 10 chrV…        1 3.08e7  3095846 29174676     94.8      7.54      35.3     58.3
## # ℹ 243 more rows
## # ℹ 2 more variables: filename <chr>, samp <chr>
# combine real and simulated data into one dataframe
ga5_comb_wg <- rbind(ga5_wg, ga5_sim_wg)
ga5_comb_wg
## # A tibble: 5,474 × 11
##    chr   startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq
##    <chr>    <dbl>  <dbl>    <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl>
##  1 chrI         1 2.96e7  2276751 28423668     96.0      5.74      27.2     57.8
##  2 chrII        1 2.37e7  1791949 22810471     96.3      5.65      27.2     58.7
##  3 chrI…        1 1.78e7  1368279 16754126     94.3      5.76      27.2     57.1
##  4 chrIV        1 3.42e7  2570661 32232528     94.3      5.60      27.2     57.8
##  5 chrIX        1 2.08e7  1640991 19485000     93.5      5.88      27.2     56.8
##  6 chrM         1 1.57e4    18096    14042     89.2     86.7       27.3     49.7
##  7 chrUn        1 1.99e7  1111456  9958942     50.1      4.12      27.2     36.7
##  8 chrV         1 1.56e7  1208332 14698641     94.5      5.80      27.1     57  
##  9 chrVI        1 1.88e7  1420598 17972608     95.5      5.64      27.2     58.5
## 10 chrV…        1 3.08e7  2322042 29052786     94.4      5.62      27.2     57.9
## # ℹ 5,464 more rows
## # ℹ 2 more variables: filename <chr>, samp <chr>

Add metadata

metadata <- read_tsv(metadata_file)
## Rows: 227 Columns: 16
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (9): seq_ID, pop, coord_approx, mar_fresh, notes, water_type, used_joint...
## dbl (7): GPS_north, GPS_east, PNW_independent_MvsF_c150, NorthEurope_indepen...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
metadata
## # A tibble: 227 × 16
##    seq_ID       pop   coord_approx GPS_north GPS_east mar_fresh notes water_type
##    <chr>        <chr> <chr>            <dbl>    <dbl> <chr>     <chr> <chr>     
##  1 AKMA_X_2001… Alas… <NA>              60.1  -149.   M         <NA>  Marine    
##  2 AKST_X_2001… Alas… <NA>              60.1  -149.   F         <NA>  River     
##  3 ANSR_X_2009… Anse… <NA>              54.1  -132.   F         <NA>  Freshwater
##  4 BARW_X_2012… Barr… <NA>              71.3  -157.   M         <NA>  Marine    
##  5 BHAR_X_2011… Nort… <NA>              57.6    -7.28 F         <NA>  Lake      
##  6 BIGR_1_32_2… Big … <NA>              39.3  -124.   M         <NA>  Marine    
##  7 BIGR_52_54_… Big … <NA>              39.3  -124.   F         <NA>  River     
##  8 BIGR_1_32_2… Big … <NA>              39.3  -124.   M         <NA>  Marine    
##  9 BIGR_1_32_2… Big … <NA>              39.3  -124.   M         <NA>  Marine    
## 10 BIGR_3_63_2… Big … <NA>              39.3  -124.   M         <NA>  Marine    
## # ℹ 217 more rows
## # ℹ 8 more variables: PNW_independent_MvsF_c150 <dbl>,
## #   NorthEurope_independent_MvsF_c151 <dbl>,
## #   CaliforniaFreshwater_vs_AllPacificMarine_c153 <dbl>,
## #   c154_globalsuperglacial_FvsM <dbl>, c155_global_FvsM <dbl>,
## #   used_joint_genotyping <chr>, `used _river_comparisons` <chr>,
## #   used_pilot_analysis <chr>

Is the depth consistent across chromosomes?

# Plot coverage by chromosome
ga5_wg %>% 
  filter(!chr %in% c("chrM", "chrUn")) %>% 
  ggplot(aes(chr, meandepth)) +
  geom_point() +
  coord_flip() +
  facet_wrap(~samp)

Samples that look like they are actually males:

# Plot coverage by chromosome for two normal samples and the samples that look like males
ga5_wg %>% 
  filter(!chr %in% c("chrM", "chrUn"), 
         samp %in% c("AKMA_X_2001_102", "AKST_X_2001_03", "BIGR_1_32_2007_02", "BK70_X_2010_02", "BNST_X_2006_10", "LAUR_X_1993_9_5", "MIDF_REND_2011_05", "MIDF_REND_2011_06", "NTRW_X_X_02", "REIV_X_2011_04")) %>% 
  ggplot(aes(chr, meandepth)) +
  geom_point() +
  coord_flip() +
  facet_wrap(~samp, nrow=1)

Some samples look like they have very uneven coverage…why would this be?

# get whole genome mean depth for gasAcu5 masked aligned (excluding chrUn, chrM, chrY) per sample 
ga5_wg_cov <- ga5_comb_wg %>% 
  filter(!chr %in% c("chrUn", "chrM", "chrY")) %>% 
  group_by(samp) %>% 
  summarize(weighted_mean_depth = weighted.mean(meandepth, endpos))
ga5_wg_cov
## # A tibble: 238 × 2
##    samp            weighted_mean_depth
##    <chr>                         <dbl>
##  1 AKMA_X_2001_102               5.66 
##  2 AKST_X_2001_03                6.12 
##  3 ANSR_X_2009_01               10.3  
##  4 ANTL                          0.733
##  5 BARW_X_2012_04                5.71 
##  6 BDGB                          1.46 
##  7 BEPA                          1.21 
##  8 BHAR_X_2011_02                5.21 
##  9 BIGL                          2.34 
## 10 BIGR                          1.61 
## # ℹ 228 more rows
# Add additional depth and metadata info to rois
ga5_roi_cov <- left_join(ga5_comb_roi, ga5_wg_cov) %>% 
  left_join(., metadata, by = c("samp" = "seq_ID")) %>% 
   mutate(wg_norm_depth = meandepth / weighted_mean_depth,
          ecotype = case_when(mar_fresh == "M" ~ "Marine",
                              mar_fresh == "F" ~ "Freshwater",
                              type == "sim" ~ "Simulation"),
          ecotype = as.factor(ecotype), 
         ecotype = relevel(ecotype, "Marine"),
         sex = case_when(samp %in% c("BIGR_1_32_2007_02", "BK70_X_2010_02", "BNST_X_2006_10", "LAUR_X_1993_9_5", "MIDF_REND_2011_05", "MIDF_REND_2011_06", "NTRW_X_X_02", "REIV_X_2011_04", "rabs_THREE_spine.male.fa_sim4X.rep0", "stickleback_v5-BOULxBDGB_F5-4copy.male.fa_sim4X.rep0", "stickleback_v5-BEPA-AF_ONT_M1020-5copy.male.fa_sim4X.rep0", "stickleback_v5-BLAU22_12-6copy.male.fa_sim4X.rep0") ~ "male",
                         TRUE ~ "female"),
         samp_length = str_length(samp)) %>% 
  separate(samp, into = "acronym", remove=FALSE, sep="_")
## Joining with `by = join_by(samp)`
## Warning: Expected 1 pieces. Additional pieces discarded in 1752 rows [1, 2, 3, 4, 5, 6,
## 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
ga5_roi_cov %>% 
  filter(sex=="female") %>% 
#  mutate(desc = fct_relevel(desc, "eda", "nlrc5", "calb2a")) %>% 
  ggplot(aes(reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
  geom_point() +
  scale_color_manual(values=c("#d73027","#0072b2", "black")) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0)) +
  facet_wrap(~desc, ncol = 1) +
  xlab("Individual") +
  ylab("Normalized depth (1x genome coverage)")

# Plot just the male samples for gasAcu5 masked aligned
ga5_roi_cov %>% 
  filter(sex=="male") %>% 
#  mutate(desc = fct_relevel(desc, "eda", "nlrc5", "calb2a")) %>% 
  ggplot(aes(reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
  geom_point() +
  scale_color_manual(values=c("#d73027","#0072b2", "black")) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0)) +
  facet_wrap(~desc, ncol = 11) +
  xlab("Individual") +
  ylab("Normalized depth (1x genome coverage)")

# Plot just the simulated samples for gasAcu5 masked aligned
ga5_roi_cov %>% 
  filter(type=="sim") %>% 
#  mutate(desc = fct_relevel(desc, "eda", "nlrc5", "calb2a")) %>% 
  ggplot(aes(reorder(samp, wg_norm_depth), wg_norm_depth)) +
  geom_point() +
  theme(axis.text.x=element_text(angle = -90, hjust = 0)) +
  facet_wrap(~desc, ncol = 11) +
  xlab("Individual") +
  ylab("Normalized depth (1x genome coverage)")

ga5_roi_cov %>% 
  filter(desc == "HTRA1A") %>%
  ggplot(aes(fct_reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
  geom_point() +
  scale_color_manual(values=c("#d73027","#0072b2", "black")) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0), legend.position = c(0.025, 0.75)) +
  ylim(0,3) +
  ggtitle("HTRA1 read depth") +
  xlab("Individual") +
  ylab("Normalized depth (1x genome coverage)")
## Warning: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2
## 3.5.0.
## ℹ Please use the `legend.position.inside` argument of `theme()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

# Get average from simulations
sim_average <- ga5_roi_cov %>% 
  filter(type=="sim", desc=="MYH3C3") %>% 
  mutate(CN = case_when(str_detect(samp, "3copy") ~ "3-copy",
                        str_detect(samp, "4copy") ~ "4-copy",
                        str_detect(samp, "5copy") ~ "5-copy",
                        str_detect(samp, "6copy") ~ "6-copy")) %>% 
  group_by(CN, sex) %>% 
  summarise(wg_norm_depth = mean(wg_norm_depth))
## `summarise()` has grouped output by 'CN'. You can override using the `.groups`
## argument.
sim_average
## # A tibble: 4 × 3
## # Groups:   CN [4]
##   CN     sex    wg_norm_depth
##   <chr>  <chr>          <dbl>
## 1 3-copy female         0.763
## 2 4-copy female         1.48 
## 3 5-copy female         2.33 
## 4 6-copy female         3.07
# Plot MYH3C3 read depth for all samples  
ga5_roi_cov %>% 
  filter(desc == "MYH3C3", sex=="female", type=="real") %>%
  ggplot(aes(fct_reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey") +
  geom_point() +
  scale_color_manual(values=c("#d73027","#0072b2", "black")) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0), legend.position = c(0.025, 0.75)) +
  xlab("Individual") +
  ylab("Normalized MYH3C3 read depth")

# Plot MYH3C3 read depth for all samples except those used in river comparisons
ga5_roi_cov %>% 
  filter(desc == "MYH3C3",
         sex=="female",
         type=="real",
         is.na(`used _river_comparisons`)) %>%
  ggplot(aes(fct_reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
    geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey") +
  geom_point() +
  scale_color_manual(values=c("#d73027","#0072b2", "black")) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0), legend.position = c(0.03, 0.75)) +
  xlab("Individual") +
  ylab("Normalized MYH3C3 read depth")

# Plot MYH3C3 read depth for all samples except those used in river comparisons and the low depth original Jones et al. 2012 samples
ga5_roi_cov %>% 
  filter(desc == "MYH3C3",
         sex=="female",
         type=="real",
         is.na(`used _river_comparisons`),
         samp_length > 6) %>%
  ggplot(aes(fct_reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
    geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey") +
  geom_point() +
  scale_color_manual(values=c("#d73027","#0072b2", "black")) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0), legend.position = c(0.04, 0.79)) +
  xlab("Individual") +
  ylab("Normalized MYH3C3 read depth")

# Plot MYH3C3 read depth for MAYR lake
ga5_roi_cov %>% 
  filter(desc == "MYH3C3",
         sex=="female",
         type=="real",
         acronym=="MAYR",
         samp_length > 6) %>%
  ggplot(aes(fct_reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
    geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey") +
  geom_point() +
  scale_color_manual(values=c("#0072b2")) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0), legend.position = c(0.04, 0.79)) +
  xlab("Individual") +
  ylab("Normalized MYH3C3 read depth")

# Plot MYH3C3 read depth for all samples except those used in river comparisons and the low depth original Jones et al. 2012 samples
C3_global <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3",
         sex=="female",
         type=="real",
         c155_global_FvsM %in% c(0,1),
         samp_length > 6) %>%
  ggplot(aes(fct_reorder(samp, wg_norm_depth), wg_norm_depth, color = ecotype)) +
    geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey") +
  geom_point() +
  scale_color_manual(values=c("#d73027","#0072b2", "black")) +
   theme_cowplot(6) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0), legend.position = c(0.07, 0.79)) +

  xlab("Individual") +
  ylab("Normalized MYH3C3 read depth")
C3_global

ga5_roi_cov %>% 
  filter(desc == "MYH3C3", type=="real", sex=="female", c155_global_FvsM %in% c(0,1), samp_length > 6) %>%
  ggscatter(x = "GPS_north", y = "wg_norm_depth",
   color = "ecotype", palette = c("#d73027","#0072b2"),
   add = "reg.line", conf.int = TRUE,
   xlab = "Latitude (°N)",
   ylab = "Normalized depth of MYH3C3\n(1x genome coverage)") + 
  stat_cor(aes(color = ecotype), label.x = 30) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey")

Pacific_PNW_lat <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", PNW_independent_MvsF_c150 %in% c(0,1), samp_length > 6) %>%
  ggscatter(x = "GPS_north", y = "wg_norm_depth",
   color = "ecotype", palette = c("#d73027","#0072b2"),
   add = "reg.line", conf.int = TRUE,
   xlab = "Latitude",
   ylab = "Normalized depth of MYH3C3") + 
  stat_cor(aes(color = ecotype)) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey")
Pacific_PNW_lat

# Plot without original 21 genomes and including California
Pacific_CA_lat <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", PNW_independent_MvsF_c150 %in% c(0,1) | CaliforniaFreshwater_vs_AllPacificMarine_c153 %in% c(0,1), samp_length > 6) %>%
  ggscatter(x = "GPS_north", y = "wg_norm_depth",
   color = "ecotype", palette = c("#d73027","#0072b2"),
   add = "reg.line", conf.int = TRUE,
   xlab = "Latitude",
   ylab = "Normalized depth of MYH3C3") + 
  stat_cor(aes(color = ecotype))+
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey")

Pacific_CA_lat

# Plot without original 21 genomes and for populations glaciated during the last ice age
ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", c154_globalsuperglacial_FvsM %in% c(0,1), samp_length > 6) %>%
  ggscatter(x = "GPS_north", y = "wg_norm_depth",
   color = "ecotype", palette = c("#d73027","#0072b2"),
   add = "reg.line", conf.int = TRUE,
   xlab = "Latitude",
   ylab = "Normalized depth of MYH3C3\n(1x genome coverage)") + 
  stat_cor(aes(color = ecotype)) +
      geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey")

# Plot without original 21 samples
Europe_lat <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", NorthEurope_independent_MvsF_c151 %in% c(0,1), samp_length > 6) %>%
  ggscatter(x = "GPS_north", y = "wg_norm_depth",
   color = "ecotype", palette = c("#d73027","#0072b2"),
   add = "reg.line", conf.int = TRUE,
   xlab = "Latitude",
   ylab = "MYH3C3 normalized depth") + 
  stat_cor(aes(color = ecotype)) +
      geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey")
Europe_lat

# Plot without original 21 samples
test <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", c155_global_FvsM %in% c(0,1), samp_length >6) %>%
  ggplot(aes(ecotype, wg_norm_depth, color = ecotype)) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey") +
  geom_beeswarm(size = 3, cex=2.5,alpha = 0.7) +
  geom_boxplot(fill = NA) +
  scale_color_manual(values=c("#d73027","#0072b2")) +
  xlab("Ecotype") +
  ylab("MYH3C3 normalized depth") +
  theme_cowplot(6) +
    theme(legend.position = "top") +
  stat_compare_means(aes(group = ecotype), label.x = 1, label.y = 2.6, size = 3)
test

ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", str_detect(samp, "LOBG")) %>%
  ggplot(aes(pop, wg_norm_depth, color = pop)) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey") +
  geom_beeswarm(size = 3, cex=2.5,alpha = 0.7) +
  geom_boxplot(fill = NA) +
  scale_color_manual(values=c("#d73027","#0072b2")) +
  ggtitle("MYH3C3 read depth") +
  xlab("Ecotype") +
  ylab("Normalized depth of MYH3C3 \n(1x genome coverage)") +
  theme(legend.position = "none",
        text = element_text(size=16)) +
  stat_compare_means(aes(group = ecotype), label.x = 1, label.y = 2.6, size = 5)
## Warning: Unknown or uninitialised column: `p`.
## Warning: Computation failed in `stat_compare_means()`.
## Caused by error:
## ! argument "x" is missing, with no default

# Make wider version of table to plot correlation between different genes
ga5_roi_cov_wide <- ga5_roi_cov %>% 
  select(desc, samp:type, weighted_mean_depth:sex) %>% 
  pivot_wider(names_from = desc, values_from = wg_norm_depth)
# Plot pearson correlation between MYH3C3 read depth and duplication region
ga5_roi_cov_wide %>% 
  filter(sex=="female", type=="real") %>%
  ggscatter(x = "MYH3C3", y = "duplication_region",
   add = "reg.line", conf.int = TRUE, alpha=0.5) +
  stat_cor()

Final figure plots

# Plot MYH3C3 read depth for balanced global selection, excluding low depth original Jones et al. 2012 samples
ga5_roi_cov_filt <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", NorthEurope_independent_MvsF_c151 %in% c(0,1)|PNW_independent_MvsF_c150 %in% c(0,1)|CaliforniaFreshwater_vs_AllPacificMarine_c153 %in% c(0,1), samp_length > 6) %>%
  mutate(Individual = case_when(samp == "BIGR_1_32_2007_03" ~ "BIGR_M",
                                samp == "BIGR_52_54_2008_02" ~ "BIGR_F",
                                samp == "LITC_0_05_2008_841" ~ "LITC_M",
                                samp == "LITC_23_32_2008_306" ~ "LITC_F",
                                samp == "MIDF_BLUP_2011_01" ~ "MIDF_M",
                                samp == "MIDF_REND_2011_01" ~ "MIDF_F",
                                samp == "TYNE_1_2001_14" ~ "TYNE_M",
                                samp == "TYNE_8_2003_902" ~ "TYNE_F",
                                TRUE ~ acronym))
# Wilcoxon test for marine vs freshwater
w <- wilcox.test(subset(ga5_roi_cov_filt, ecotype == "Freshwater")$wg_norm_depth, subset(ga5_roi_cov_filt, ecotype == "Marine")$wg_norm_depth, alternative = "greater")
w
## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  subset(ga5_roi_cov_filt, ecotype == "Freshwater")$wg_norm_depth and subset(ga5_roi_cov_filt, ecotype == "Marine")$wg_norm_depth
## W = 1211, p-value = 4.917e-08
## alternative hypothesis: true location shift is greater than 0
C3_global <- ga5_roi_cov_filt %>% 
  ggplot(aes(fct_reorder(Individual, wg_norm_depth), wg_norm_depth, color = ecotype)) +
    geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey", linewidth=0.25) +
  geom_segment( aes(x=Individual, xend=Individual, y=0, yend=wg_norm_depth)) +
  geom_point(size=1.5) +
  scale_color_manual(values=c("#d73027","#0072b2"), name = "Ecotype") +
#  scale_shape_manual(values = c(21,19)) +
  scale_y_continuous(limits = c(0,3.7), expand = expansion(mult = c(0, 0))) +
   theme_cowplot(6) +
    panel_border(color="black", size=0.75) +
  theme(axis.text.x=element_text(angle = -90, hjust = 0), 
        legend.position = c(0.02, 0.8),
        legend.box.background = element_rect(color="black", linewidth=0.25, fill = "white"),
      legend.box.margin = margin(4, 4, 4, 4)) +
  xlab("Individual") +
  ylab("MYH3C3 normalized depth")
#    ylim(0,3.5)
C3_global

# Plot with facet
lat <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3",  type=="real", sex=="female", NorthEurope_independent_MvsF_c151 %in% c(0,1)|PNW_independent_MvsF_c150 %in% c(0,1)|CaliforniaFreshwater_vs_AllPacificMarine_c153 %in% c(0,1), samp_length > 6) %>%
  mutate(ocean = case_when(PNW_independent_MvsF_c150 %in% c(0,1)|CaliforniaFreshwater_vs_AllPacificMarine_c153 %in% c(0,1) ~ "Pacific",
                           NorthEurope_independent_MvsF_c151 %in% c(0,1) ~ "Atlantic")) %>% 
  ggplot(aes(GPS_north, wg_norm_depth, color = ecotype)) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey", linewidth=0.25) +
  geom_point(alpha=0.7, size=1.5) +
  geom_smooth(aes(fill = ecotype), method = "lm") +
  stat_cor(aes(color = ecotype), size=2) +
  scale_color_manual(values=c("#d73027","#0072b2"),) +
  scale_fill_manual(values=c("#d73027","#0072b2")) +
  scale_y_continuous(limits = c(0,3.7), expand = expansion(mult = c(0, 0))) +
  facet_wrap(~factor(ocean, levels=c("Pacific", "Atlantic")), scales = "free_x") +
  theme_cowplot(6) +
  panel_border(color="black", size=0.75) +
  theme(legend.position = "none") +
  xlab("Latitude (°N)") +
  ylab("MYH3C3 normalized depth")
  
lat
## `geom_smooth()` using formula = 'y ~ x'

hz_plot <- ga5_roi_cov %>% 
  filter(desc == "MYH3C3", sex == "female", !is.na(`used _river_comparisons`), samp_length > 6) %>% 
  mutate(location = as.factor(case_when(acronym == "BIGR" ~ "Big River,\nCA, USA",
                              acronym %in% c("BNMA", "BNST") ~ "Bonsall River,\nBC, Canada",
                              acronym == "LITC" ~ "Little Campbell River,\nBC, Canada",
                              acronym == "TYNE" ~ "Tyne River,\nScotland, UK",
                              acronym == "MIDF" ~ "Midfjardara River,\nIceland")),
         location = fct_relevel(location, "Big River,\nCA, USA", "Little Campbell River,\nBC, Canada", "Bonsall River,\nBC, Canada", "Tyne River,\nScotland, UK", "Midfjardara River,\nIceland")) %>% 
  ggplot(aes(location, wg_norm_depth, color = ecotype)) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey", linewidth=0.25) +
  geom_beeswarm(cex=2, dodge.width = .7, alpha = 0.7) +
  geom_boxplot(fill = NA, outlier.shape = NA) +
  scale_color_manual(values=c("#d73027","#0072b2")) +
  scale_y_continuous(limits = c(0,3.7), expand = expansion(mult = c(0, 0))) +
#  ylim(0,2.5) +
  ylab("MYH3C3 normalized depth") +
  theme_cowplot(6) +
  panel_border(color="black", size=0.75) +
  theme(legend.position = "none",
        axis.title.x=element_blank()) +
  stat_compare_means(aes(group = ecotype), label.x = 1, label.y = 3.3, size = 3, label="p.signif")
hz_plot

# Arrange plots using cowplot
# align all plots vertically
plots <- align_plots(test, C3_global, lat, hz_plot, align = 'v', axis = 'l')
## `geom_smooth()` using formula = 'y ~ x'
top_row <- plot_grid(
  plots[[2]],
  labels = c("B"),
  label_size = 12,
  nrow = 1
)

bottom_row <- plot_grid(
  plots[[3]], plots[[4]],
  labels = c("C", "D"),
  rel_widths = c(1, 1),
  label_size = 12,
  nrow = 1
)
final_plot <- plot_grid(top_row, bottom_row, ncol = 1, rel_heights = c(1.1, 1), label_size = 12)
final_plot

# Save ASE figure to separate file
ggsave(
  "/labs/kingsley/ambenj/myosin_dups/analysis/ecotypic_depth/gasAcuv5_C4masked_nochrY/ecotypic_depth_figure.pdf",
  plot = final_plot,
  scale = 1,
  width = 6.5,
  height = 3.75,
  units = c("in"),
  dpi = 300,
)

PCA of myosin region

# Reformat (biallelic version, can also try "copy.num.of.ref")
snpgdsVCF2GDS(vcf_file_1, "all.gds", method="biallelic.only")
## Start file conversion from VCF to SNP GDS ...
## Method: extracting biallelic SNPs
## Number of samples: 227
## Parsing "/labs/kingsley/ambenj/myosin_dups/analysis/assemblies/gasAcu1-4/227_genomes.final.filtered.MYHSensitiveEcopeak.noDup.recode.vcf" ...
##  import 3570 variants.
## + genotype   { Bit2 227x3570, 197.8K } *
## Optimize the access efficiency ...
## Clean up the fragments of GDS file:
##     open the file 'all.gds' (221.0K)
##     # of fragments: 47
##     save to 'all.gds.tmp'
##     rename 'all.gds.tmp' (220.7K, reduced: 324B)
##     # of fragments: 20
# Summary
snpgdsSummary("all.gds")
## The file name: /oak/stanford/scg/lab_kingsley/ambenj/myosin_dups/scripts/R/all.gds 
## The total number of samples: 227 
## The total number of SNPs: 3570 
## SNP genotypes are stored in SNP-major mode (Sample X SNP).
# Open GDS file
genofile <- snpgdsOpen("all.gds")

genofile
## File: /oak/stanford/scg/lab_kingsley/ambenj/myosin_dups/scripts/R/all.gds (220.7K)
## +    [  ] *
## |--+ sample.id   { Str8 227 LZMA_ra(35.7%), 1.2K }
## |--+ snp.id   { Int32 3570 LZMA_ra(12.8%), 1.8K }
## |--+ snp.rs.id   { Str8 3570 LZMA_ra(2.97%), 113B }
## |--+ snp.position   { Int32 3570 LZMA_ra(27.8%), 3.9K }
## |--+ snp.chromosome   { Str8 3570 LZMA_ra(0.94%), 141B }
## |--+ snp.allele   { Str8 3570 LZMA_ra(15.4%), 2.1K }
## |--+ genotype   { Bit2 227x3570, 197.8K } *
## \--+ snp.annot   [  ]
##    |--+ qual   { Float32 3570 LZMA_ra(82.8%), 11.6K }
##    \--+ filter   { Str8 3570 LZMA_ra(0.80%), 149B }
# Run PCA
pca <- snpgdsPCA(genofile, num.thread=2, autosome.only = FALSE)
## Principal Component Analysis (PCA) on genotypes:
## Excluding 11 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
##     # of samples: 227
##     # of SNPs: 3,559
##     using 2 threads
##     # of principal components: 32
## PCA:    the sum of all selected genotypes (0,1,2) = 1237565
## CPU capabilities: Double-Precision SSE2
## Sun Jul 13 22:16:21 2025    (internal increment: 4292)
## [..................................................]  0%, ETC: ---        [==================================================] 100%, completed, 0s
## Sun Jul 13 22:16:21 2025    Begin (eigenvalues and eigenvectors)
## Sun Jul 13 22:16:21 2025    Done.
#pca_filter <- snpgdsPCA(genofile, num.thread=2, autosome.only = FALSE, sample.id = vcf_samples_filt)

snpgdsClose(genofile)
# variance proportion (%)
pc.percent <- round(pca$varprop*100, 2)
PC1_lab <- paste("PC1 (", pc.percent[1], "%)", sep = "")
PC2_lab <- paste("PC2 (", pc.percent[2], "%)", sep = "")
# make a data.frame
tab <- data.frame(sample.id = pca$sample.id,
    EV1 = pca$eigenvect[,1],    # the first eigenvector
    EV2 = pca$eigenvect[,2],    # the second eigenvector
    EV3 = pca$eigenvect[,3],    # the third eigenvector
    EV4 = pca$eigenvect[,4],    # the fourth eigenvector
    stringsAsFactors = FALSE)

tab_annot <- tab %>%
  mutate(samp = str_replace_all(sample.id, '\\|', '_'),
         samp = str_replace_all(samp, '\\#', '_')) %>%
  left_join(., filter(ga5_roi_cov, desc == "MYH3C3"), by=c("samp" = "samp")) %>% 
  left_join(., read_tsv(het_file), by=c("sample.id" = "INDV")) %>% 
  mutate(prop_hom = `O(HOM)`/N_SITES,
         prop_het = 1-prop_hom,
         het_status = ifelse(F > 0.5, "likely-hom", "likely-het"))
## Rows: 227 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (1): INDV
## dbl (4): O(HOM), E(HOM), N_SITES, F
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
tab_annot
##               sample.id           EV1          EV2           EV3           EV4
## 1       AKMA|X|2001#102  0.1229973506 -0.036164554  0.0078482840 -5.829536e-03
## 2        AKST|X|2001#03 -0.0540685701 -0.024170294  0.0154518328 -2.967874e-03
## 3        ANSR_X_2009#01 -0.0488148378 -0.020515347  0.0134344962 -2.303888e-03
## 4                  ANTL  0.0011383959 -0.007256721  0.0027692207  1.486978e-04
## 5        BARW|X|2012#04  0.1203047443 -0.036465805  0.0068169850  1.544402e-03
## 6                  BDGB  0.0107605097 -0.010982033  0.0075335915 -2.826808e-03
## 7                  BEPA -0.0326665285 -0.013685672  0.0079011114 -6.228288e-05
## 8        BHAR|X|2011#02  0.1255649180 -0.043802700  0.0055753083  3.035664e-03
## 9                  BIGL -0.0146005684  0.044801849  0.0143877877 -3.729064e-03
## 10                 BIGR -0.0129065216  0.023308549  0.0090199669  9.761090e-03
## 11    BIGR_1_32_2007#03  0.0100751593  0.115785628  0.0183156456 -1.042762e-01
## 12   BIGR_52_54_2008#02  0.0091435651  0.144795196  0.0263159483  2.408555e-01
## 13    BIGR|1_32|2007#01  0.0188560556  0.163583424  0.0278809268 -7.274894e-02
## 14    BIGR|1_32|2007#02  0.0096217805  0.132945593 -0.4035082338 -1.201959e-01
## 15    BIGR|3_63|2007#08  0.0539102017  0.072841120  0.0179592043 -1.438120e-02
## 16    BIGR|3_63|2007#14  0.0162503009  0.164434928  0.0344149784  1.335552e-02
## 17   BIGR|52_54|2007#04  0.0199480738  0.201728347  0.0330942137  3.714994e-01
## 18   BIGR|52_54|2007#05  0.0168073085  0.199775348  0.0325064511  3.498671e-01
## 19   BIGR|52_54|2007#12  0.0204752622  0.188043740  0.0337738891  1.870450e-01
## 20   BIGR|52_54|2007#17  0.0193218937  0.203851980  0.0323342876  3.709131e-01
## 21          BITJ|X|X#17  0.1346372052 -0.048492985  0.0040052506  3.326175e-03
## 22       BK70_X_2010#02 -0.0283131466 -0.005219098 -0.1517376652  9.148944e-04
## 23       BKW2_X_2010#01 -0.0515444654 -0.023705532  0.0149340190 -2.477336e-04
## 24       BLAU|X|2002#08 -0.0533887089 -0.025331736  0.0003418651  5.497741e-03
## 25       BNMA|X|2006#01  0.1208561114 -0.035868220  0.0072909423 -6.392751e-03
## 26       BNMA|X|2006#02  0.0184182283 -0.026312279  0.0121381272 -1.900110e-03
## 27       BNMA|X|2006#03  0.0535496055  0.070169853  0.0113359189  8.263133e-02
## 28       BNMA|X|2006#05  0.1126502304 -0.034097088  0.0070829646  4.879090e-03
## 29       BNMA|X|2006#07  0.1135331914 -0.032266081  0.0064769735 -2.671297e-03
## 30        BNST|X2006#08 -0.0529718339 -0.024397827  0.0137248419 -3.288410e-04
## 31       BNST|X|2006#01 -0.0529862572 -0.024345390  0.0135640139 -9.531572e-04
## 32       BNST|X|2006#06 -0.0525914568 -0.024007193  0.0131488791 -4.456826e-04
## 33       BNST|X|2006#09 -0.0512432789 -0.022789173  0.0138752525  1.516363e-03
## 34       BNST|X|2006#10  0.0099585403  0.121795420 -0.3909912501  1.226684e-01
## 35       BOOT|X|2011#05 -0.0537923751 -0.023945030  0.0124212473 -3.239073e-04
## 36       BOUL_X_2010#01 -0.0554163990 -0.024579621  0.0130122832  3.423150e-04
## 37       BOUL_X_2010#02 -0.0546592346 -0.024001761  0.0122813819  5.449902e-04
## 38       BRLY|X|2012#01 -0.0529800504 -0.023330502  0.0138376564 -2.540152e-04
## 39       BRNT_X_2009#05 -0.0537791757 -0.023642201  0.0151197604 -6.788869e-04
## 40      BSEA|55|2011#01  0.1146099896 -0.032726173  0.0012339467 -2.822104e-03
## 41          CERC|X|X#04  0.0150473718  0.181450131  0.0266545316 -1.619563e-01
## 42       CHRU|X|2011#04 -0.0472742454 -0.023408963  0.0074123675  2.322476e-03
## 43       CMCB|X|2011#02 -0.0511776015 -0.021976694  0.0123998837 -8.962840e-04
## 44    COAT|X|2009#90234 -0.0544979801 -0.024109283  0.0134946980  2.058328e-04
## 45       COND|X|2002#14 -0.0165439282  0.054370003  0.0059781057  1.197715e-02
## 46       CORC|X|2011#01 -0.0538772484 -0.024066537  0.0147682569 -2.535499e-03
## 47       DAIM|X|2011#03 -0.0485920578 -0.023510551  0.0075031240  1.374020e-03
## 48          DANS|X|X#05 -0.0536869287 -0.022934091  0.0146383326 -4.918477e-04
## 49       DARW_X_2009#03  0.1221097573 -0.037327091  0.0056668373  1.784648e-03
## 50       DAWS_X_2009#02  0.1212210407 -0.039273920  0.0079360364 -3.933452e-03
## 51       DNSE|X|2011#07 -0.0539374615 -0.024327501  0.0108074822 -1.343635e-03
## 52       DRIZ_I_2010#01 -0.0539405025 -0.022378795  0.0146928717 -3.882860e-03
## 53       DRIZ_L_2009#02 -0.0543924964 -0.024114791  0.0147243476 -3.909349e-04
## 54       DRIZ_L_2009#15 -0.0543716626 -0.023402939  0.0143440581 -9.711323e-04
## 55       DRIZ_O_2009#03 -0.0546591182 -0.024216776  0.0145536656 -1.757859e-04
## 56       ECHO|X|2011#03 -0.0526502771 -0.023792102  0.0130957275 -6.015032e-04
## 57       EDEN_X_2010#01 -0.0545903673 -0.023886257  0.0133033399  9.069261e-04
## 58        ERBC|X|X#8770  0.0218436125  0.199461326  0.0233117106 -2.013031e-01
## 59     ESCP|X|1993#75_8 -0.0529991857 -0.024039468  0.0128710847  7.328591e-04
## 60      FADA_FJ_2001#17  0.1234581311 -0.043492981  0.0033309470  3.536780e-03
## 61      FRIC_X_2003#C10  0.0210042351  0.186926137  0.0333053677 -2.363568e-01
## 62          FRIL|X|X#05  0.0220998474  0.197572307  0.0314944070 -2.462027e-01
## 63                  FTC -0.0450298157 -0.018586042  0.0108523618  1.868220e-04
## 64         GARC|X|X#711  0.0171456832  0.193255122  0.0268114408 -1.832810e-01
## 65       GIFU|X|2000#03  0.0344312621 -0.018539311 -0.0148748179 -9.878367e-03
## 66                 GJOG  0.0126323868 -0.015858257  0.0068858055  8.668851e-04
## 67       GOLD_X_2009#02 -0.0550466419 -0.023966956  0.0148388445 -5.511251e-04
## 68          GOLD|X|X#12 -0.0538821254 -0.023721245  0.0140645557 -6.686325e-04
## 69                 GORT  0.0117742608 -0.014586619  0.0071487048  1.640883e-03
## 70          HRUN|X|X#02 -0.0522988712 -0.025186502  0.0020171448  4.783066e-03
## 71       HSTA|X|2011#03  0.1201473600 -0.046694824  0.0041802924  2.758695e-03
## 72                 HUTU -0.0411524933 -0.010459260 -0.0046190031 -3.068075e-03
## 73       JADE|X|2011#05 -0.0542258002 -0.023775805  0.0149158665 -1.057878e-03
## 74                 JAMA  0.0179212208 -0.016033945  0.0078648278 -1.362649e-03
## 75       KALD|X|2010#03  0.1195940425 -0.045219893  0.0033144384  2.837464e-03
## 76       KFSY|X|2011#05 -0.0542054499 -0.023424570  0.0154360662 -1.815958e-03
## 77       KODK|X|2004#04  0.1205462090 -0.038354471  0.0090635596 -6.057208e-03
## 78       LAMH|X|2001#09  0.1198858623 -0.044161032  0.0049028973  2.977919e-03
## 79       LANO|X|2001#05  0.1301576262 -0.045422110  0.0039122304  5.373039e-03
## 80      LAUR|X|1993#9_5 -0.0397689507  0.001839763 -0.3877767113  4.616418e-03
## 81   LITC_0_05_2008#841  0.0824038832 -0.022602518  0.0074676941 -7.694479e-04
## 82   LITC_0_05_2008#842  0.1006939327 -0.029728891  0.0083962867 -8.215602e-03
## 83    LITC_0_05_2008#FL  0.0598516612 -0.019483763  0.0080299973 -7.095817e-03
## 84    LITC_0_05_2008#FO  0.0933551100 -0.027439810  0.0077745078 -1.881018e-03
## 85   LITC_0_45_2008#789  0.1100719330 -0.031031553  0.0087006289 -5.269072e-03
## 86  LITC_23_32_2008#306 -0.0514082072 -0.023220768  0.0128376143  6.586722e-04
## 87  LITC_23_32_2008#324 -0.0514211599 -0.022351299  0.0139097974  1.058069e-03
## 88  LITC_23_32_2008#347 -0.0492161275 -0.021898513  0.0124763258 -7.291652e-04
## 89  LITC_23_32_2008#356 -0.0538756467 -0.023869897  0.0136214212  4.280138e-04
## 90  LITC_23_32_2008#744 -0.0480746753 -0.020886640  0.0136387262 -3.164768e-04
## 91       LLYD|X|2003#03  0.1341702214 -0.046180063  0.0029823540 -4.424733e-04
## 92          LMCK|X|X#03 -0.0536085538 -0.023355038  0.0155885846 -2.926902e-03
## 93          LMIA|X|X#02 -0.0491031542 -0.022586274  0.0059791697  2.468869e-03
## 94       LMOR|X|2001#12  0.1411295477 -0.049419539  0.0050817848  2.713848e-03
## 95       LNEA|M|2001#03 -0.0506689379 -0.023968727  0.0049919401  3.286377e-04
## 96       LNGH|X|2011#01 -0.0477761230 -0.022691217  0.0067536914  1.801911e-03
## 97       LOBG|X|1999#09  0.0188487824 -0.030340851  0.0109251693 -2.224118e-03
## 98       LOBG|X|1999#11  0.0188761398 -0.029952313  0.0114392873 -8.916531e-04
## 99       LOBG|X|1999#12 -0.0549376683 -0.024633472  0.0154262737  4.649244e-04
## 100      LOBG|X|1999#13  0.0216457047 -0.031999913  0.0124611879 -5.515466e-03
## 101      LOBG|X|1999#32  0.1274285075 -0.039904049  0.0062832994 -5.545157e-03
## 102      LOBG|X|1999#36  0.0197616971 -0.031386905  0.0099676992 -4.854873e-04
## 103      LOBG|X|1999#38 -0.0545691675 -0.024466393  0.0154091014 -2.215222e-03
## 104      LOBG|X|1999#39 -0.0545797410 -0.024727973  0.0150833629 -1.285857e-03
## 105      LOBG|X|1999#43  0.0168090077 -0.029772543  0.0116109170 -2.119536e-03
## 106      LOBG|X|1999#46  0.1221599096 -0.039180276  0.0078398469 -2.643573e-03
## 107      LOBG|X|2012#02  0.0151026709 -0.030879997  0.0093240564 -3.595356e-03
## 108      LOBG|X|2012#03  0.0162657384 -0.031676713  0.0106977770 -2.394643e-04
## 109      LOBG|X|2012#04  0.0175649445 -0.032833888  0.0102746698 -6.026403e-04
## 110      LOBG|X|2012#05  0.0197965176 -0.033475537  0.0100408700 -1.041734e-03
## 111      LOBG|X|2012#06 -0.0531329345 -0.023854646  0.0150194745  1.233439e-04
## 112      LOBG|X|2012#08  0.0158972062 -0.030004031  0.0080919255 -1.575447e-04
## 113      LOBG|X|2012#11  0.0183350649 -0.029153647  0.0099840714 -2.340545e-03
## 114      LOBG|X|2012#17  0.1293235720 -0.036736327  0.0051465189  1.262938e-03
## 115      LOBG|X|2012#26 -0.0547043270 -0.024746457  0.0153238845  1.240199e-03
## 116      LOBG|X|2012#28 -0.0530485766 -0.023889090  0.0155534302 -2.691765e-03
## 117      LONG|X|2011#01 -0.0540299851 -0.023854379  0.0150967490 -2.413141e-04
## 118      LSHP|X|2011#01 -0.0545186964 -0.024686819  0.0153740582 -3.343674e-04
## 119      LSOL|X|2012#04  0.0179523696  0.188140675  0.0298965616 -9.516079e-02
## 120      LSWL|X|2011#05  0.1219687261 -0.043192268  0.0064893072  2.815703e-03
## 121      LTLT|X|2011#06  0.1252918284 -0.048155517  0.0042314494  2.433812e-03
## 122    LUTE|X|2003#76_4 -0.0530458790 -0.023599776  0.0142530186 -6.539849e-04
## 123         MANC|X|X#05  0.1273952564 -0.035381704  0.0070818148 -9.624805e-04
## 124                MATA -0.0146244603  0.041602369  0.0096448740  3.338899e-02
## 125      MAYR_X_2009#05 -0.0543291135 -0.024619912  0.0145727108  2.771166e-05
## 126      MAYR_X_2009#11 -0.0533908849 -0.023817174  0.0141142778 -1.015736e-03
## 127      MAYR|X|2004#03 -0.0546484546 -0.024315798  0.0148621449 -4.636820e-04
## 128      MAYR|X|2004#04 -0.0545867628 -0.024553022  0.0150553046 -4.503567e-04
## 129      MAYR|X|2004#09 -0.0546152015 -0.024555665  0.0144160149 -5.120682e-04
## 130      MAYR|X|2004#13 -0.0542225823 -0.024196477  0.0144950603 -4.270297e-04
## 131      MAYR|X|2004#14 -0.0556696099 -0.024821896  0.0143215356 -1.158318e-05
## 132      MAYR|X|2004#17 -0.0547633043 -0.024023120  0.0139654990 -2.235552e-04
## 133      MAYR|X|2004#21 -0.0534549533 -0.024030085  0.0147299548 -1.547950e-03
## 134      MAYR|X|2004#24 -0.0541329258 -0.023449081  0.0156478145 -2.122685e-03
## 135      MAYR|X|2004#26 -0.0553860723 -0.024682910  0.0136718948 -1.018044e-03
## 136      MAYR|X|2004#30 -0.0546858628 -0.024049248  0.0152484419 -5.382417e-04
## 137      MDPC_X_1993#01  0.1221369408 -0.035079671  0.0093607112 -5.148071e-03
## 138   MIDF|BDVW|2011#01  0.1288056360 -0.045787672  0.0044438622  3.179096e-03
## 139   MIDF|BDVW|2011#02  0.1215247248 -0.043578414  0.0057871196  2.670490e-03
## 140   MIDF|BLUP|2011#01  0.1276349014 -0.044915830  0.0023601099  4.398966e-03
## 141   MIDF|REND|2011#01 -0.0527109886 -0.024553967  0.0002417791  5.161337e-03
## 142   MIDF|REND|2011#04 -0.0523874580 -0.024791347  0.0002892275  4.492321e-03
## 143   MIDF|REND|2011#05 -0.0378162539  0.001327743 -0.3630701841  2.909402e-03
## 144   MIDF|REND|2011#06 -0.0369577664  0.002129532 -0.3977887358  1.176006e-03
## 145   MIDF|REND|2011#10 -0.0530082446 -0.024739161 -0.0011919452  3.103180e-03
## 146   MIDF|S101|2011#05  0.1340617609 -0.048516645  0.0027759198  4.824048e-03
## 147   MIDF|S101|2011#06  0.1219804840 -0.042971945  0.0051715352  1.847599e-03
## 148         MNKA|X|X#02 -0.0537144601 -0.024011742  0.0153993810 -1.341745e-03
## 149      MNYN|X|X#29997 -0.0539172320 -0.024549142  0.0154611457 -1.076145e-03
## 150                MUDL -0.0362087366 -0.014598379  0.0105827350 -5.469889e-04
## 151                 NEU -0.0004348792 -0.001741896 -0.0003003470 -7.818434e-08
## 152      NHBR|X|2003#05  0.1343332453 -0.044036640  0.0027895381  1.843385e-03
## 153                NOST -0.0129257638 -0.005508874  0.0025932446  1.097840e-03
## 154         NTRW|X|X#02  0.0615196477 -0.013067369 -0.2445474850  5.805627e-03
## 155      OBSE|X|2011#05  0.1260187910 -0.044039467  0.0044400565  2.278548e-03
## 156      OLNY_X_2007#03  0.0061191064  0.089801879  0.0200339388 -1.017618e-01
## 157      ORPH|X|2011#05 -0.0527867581 -0.023318379  0.0135834121  1.987529e-04
## 158                PAXB -0.0385152486 -0.015429982  0.0109726455 -1.180371e-03
## 159         PINC|X|X#03  0.0165511404  0.181985844  0.0280113570 -1.785564e-01
## 160   POQU|X|2009#29995  0.1158296486 -0.037573652  0.0073528385 -4.911781e-03
## 161      QUIN_X_2003#02 -0.0396555673 -0.011087627 -0.0124920922 -3.443325e-03
## 162                RABS  0.0427617896 -0.021475673  0.0076283003 -3.216202e-05
## 163      RCAL|X|2001#24 -0.0511533879 -0.023190643  0.0002052008 -6.553078e-05
## 164      RDSP_X_2010#02 -0.0543239223 -0.024002994  0.0145644988 -3.017552e-04
## 165   RDSP|X|2012#70307 -0.0553133333 -0.024538213  0.0147432766 -9.149840e-04
## 166   RDSP|X|2012#70311 -0.0519428548 -0.022710912  0.0119789488 -1.395656e-03
## 167   RDSP|X|2012#70314 -0.0531178033 -0.024296077  0.0144699062 -3.074004e-04
## 168   RDSP|X|2012#70332 -0.0538035786 -0.023895006  0.0145725536 -4.707764e-04
## 169   RDSP|X|2012#70337 -0.0536995371 -0.023852563  0.0149776593 -1.038817e-03
## 170   RDSP|X|2012#70346 -0.0537310332 -0.024138227  0.0141448408 -9.914177e-04
## 171   RDSP|X|2012#70353 -0.0527601710 -0.022827588  0.0150099982 -1.705027e-03
## 172   RDSP|X|2012#70364 -0.0487828462 -0.022372891  0.0147039512 -1.806339e-03
## 173   RDSP|X|2012#70368 -0.0541435589 -0.024288322  0.0148096487 -1.004834e-03
## 174   RDSP|X|2012#70385 -0.0548325594 -0.024624477  0.0149252752 -6.872845e-04
## 175      REIV|X|2011#04 -0.0043821176 -0.014494088 -0.3355559907  8.309768e-03
## 176      RGLN|X|2011#04 -0.0470000637 -0.021420364  0.0043038152  3.995610e-03
## 177     ROUG|X|2000#f03 -0.0543993759 -0.023976501  0.0145950898  1.397784e-03
## 178    SACK|X|2010#0898  0.0173504106  0.171998509  0.0284039902  2.255911e-01
## 179                SALR  0.0056227378 -0.009007944  0.0061523099 -2.313452e-04
## 180         SALS|X|X#01  0.0181552697  0.181022285  0.0282870812 -6.651498e-02
## 181         SAPC|X|X#01  0.0196026242  0.189444659  0.0305258197 -1.992952e-01
## 182     SCRM|X|2010#873  0.0161646657  0.174950119  0.0398962466  7.423526e-02
## 183    SCRS|X|2009#8253  0.0176966730  0.191527324  0.0443751987  1.021591e-01
## 184                 SCX -0.0296059448 -0.012660128  0.0055928598  6.513099e-04
## 185      SDPY_X_2006#24 -0.0544893081 -0.024130390  0.0128986189  1.217778e-03
## 186                SHEL -0.0376379989 -0.015407154  0.0068247791  4.824211e-04
## 187      SHEL_L_2008#01 -0.0457973371 -0.021009936  0.0047979028  8.453732e-04
## 188    SJCR|X|2009#8212  0.0181230015  0.169225007  0.0371114665  4.985315e-02
## 189      SKID_X_2009#01 -0.0540699925 -0.024307124  0.0145563667 -2.585706e-04
## 190         SKON|X|X#12 -0.0540916283 -0.024004917  0.0143760734 -2.692839e-05
## 191    SLMW|X|2001#0918  0.0142021341  0.170061571  0.0381698220  7.694062e-02
## 192      SLTC|X|X#90458 -0.0545302965 -0.023979041  0.0151563429 -5.011579e-04
## 193   SLVR|X|2009#29996 -0.0524237621 -0.023244845  0.0137386238 -2.534658e-03
## 194      SPNC_L_2009#01  0.0229204239 -0.031064612  0.0110028176 -3.147588e-03
## 195      SPNC_L_2009#02  0.1236537330 -0.037970157  0.0053251730 -6.999372e-03
## 196      SPNC_O_2010#08 -0.0537737420 -0.023580248  0.0134936717 -1.836477e-04
## 197      SPNC_O_2010#14 -0.0539744755 -0.024187565  0.0152573685 -4.930224e-04
## 198      SRLY|X|2011#01 -0.0543868276 -0.023660655  0.0129955083 -5.262443e-04
## 199     SRST|S1|2000#05 -0.0512944947 -0.021221098  0.0137104541 -2.590570e-03
## 200      SSMC|X|2010#01  0.0171410153  0.178347738  0.0302385646 -1.625698e-01
## 201      STIU_X_2009#03 -0.0540795444 -0.023981465  0.0153905380 -1.046128e-03
## 202      STMY|X|2011#03 -0.0538690885 -0.023705339  0.0138629855 -1.521701e-03
## 203         SUNC|X|X#04  0.0174810880  0.181743454  0.0265979662 -1.929919e-01
## 204      TERN|X|2011#02 -0.0543036522 -0.024080951  0.0154890530  3.513938e-04
## 205      TORM|X|2011#03  0.1352875342 -0.048408205  0.0046540809  4.670028e-03
## 206              TYNE_1 -0.0155822835 -0.009737746  0.0066137083  1.721318e-04
## 207      TYNE_1_2001#07  0.1250792601 -0.042873131  0.0040834768  1.132979e-03
## 208      TYNE_1_2001#08  0.1270558318 -0.043187860  0.0058939621  2.961360e-03
## 209      TYNE_1_2001#09  0.1222189641 -0.041909478  0.0050350283  1.557924e-03
## 210      TYNE_1_2001#10  0.0368497016 -0.020448130  0.0066621347 -1.757134e-05
## 211      TYNE_1_2001#14  0.1245663930 -0.044622550  0.0045116833  2.753956e-03
## 212              TYNE_8 -0.0411281632 -0.018370599  0.0087983229  2.738803e-04
## 213     TYNE_8_2003#902 -0.0479378263 -0.023876691  0.0071050538  2.869180e-03
## 214     TYNE_8_2003#906 -0.0494166718 -0.023333392  0.0075873828  1.085205e-03
## 215     TYNE_8_2003#908 -0.0514697034 -0.023840957  0.0057694274  1.838622e-03
## 216     TYNE_8_2003#919 -0.0499742114 -0.023951387  0.0058869463  2.783142e-03
## 217     TYNE_8_2003#920 -0.0483164593 -0.023715955  0.0077519857  1.420775e-03
## 218         URRI|X|X#07 -0.0526167455 -0.023567643  0.0011568094  3.475026e-03
## 219         VIFC|X|X#07 -0.0525368015 -0.024983062  0.0038021345  3.412131e-03
## 220         VIFR|X|X#08 -0.0534552539 -0.025905769  0.0035849283  2.532127e-03
## 221      WALC|X|2005#05 -0.0524548859 -0.023001474  0.0157191153 -1.769597e-03
## 222      WALR|X|2005#32 -0.0522518248 -0.023067242  0.0153355758 -3.020248e-03
## 223      WATT_X_2009#05 -0.0486892039 -0.021163281  0.0134540604 -1.014668e-04
## 224      WDPL_X_2009#05 -0.0501780091 -0.021590388  0.0141068543  2.935659e-05
## 225    WMSO_X_2002#bigf -0.0007224793  0.074346590  0.0216650424  4.705335e-02
## 226      WOLF|X|2011#04 -0.0523354208 -0.023158633  0.0149208406 -3.211175e-03
## 227      ZERO|X|2011#05 -0.0533838390 -0.023806598  0.0158872763 -1.193097e-03
##                    samp   desc                 region    chr startpos  endpos
## 1       AKMA_X_2001_102 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 2        AKST_X_2001_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 3        ANSR_X_2009_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 4                  ANTL MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 5        BARW_X_2012_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 6                  BDGB MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 7                  BEPA MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 8        BHAR_X_2011_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 9                  BIGL MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 10                 BIGR MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 11    BIGR_1_32_2007_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 12   BIGR_52_54_2008_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 13    BIGR_1_32_2007_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 14    BIGR_1_32_2007_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 15    BIGR_3_63_2007_08 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 16    BIGR_3_63_2007_14 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 17   BIGR_52_54_2007_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 18   BIGR_52_54_2007_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 19   BIGR_52_54_2007_12 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 20   BIGR_52_54_2007_17 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 21          BITJ_X_X_17 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 22       BK70_X_2010_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 23       BKW2_X_2010_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 24       BLAU_X_2002_08 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 25       BNMA_X_2006_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 26       BNMA_X_2006_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 27       BNMA_X_2006_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 28       BNMA_X_2006_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 29       BNMA_X_2006_07 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 30        BNST_X2006_08 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 31       BNST_X_2006_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 32       BNST_X_2006_06 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 33       BNST_X_2006_09 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 34       BNST_X_2006_10 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 35       BOOT_X_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 36       BOUL_X_2010_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 37       BOUL_X_2010_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 38       BRLY_X_2012_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 39       BRNT_X_2009_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 40      BSEA_55_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 41          CERC_X_X_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 42       CHRU_X_2011_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 43       CMCB_X_2011_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 44    COAT_X_2009_90234 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 45       COND_X_2002_14 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 46       CORC_X_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 47       DAIM_X_2011_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 48          DANS_X_X_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 49       DARW_X_2009_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 50       DAWS_X_2009_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 51       DNSE_X_2011_07 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 52       DRIZ_I_2010_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 53       DRIZ_L_2009_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 54       DRIZ_L_2009_15 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 55       DRIZ_O_2009_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 56       ECHO_X_2011_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 57       EDEN_X_2010_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 58        ERBC_X_X_8770 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 59     ESCP_X_1993_75_8 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 60      FADA_FJ_2001_17 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 61      FRIC_X_2003_C10 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 62          FRIL_X_X_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 63                  FTC MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 64         GARC_X_X_711 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 65       GIFU_X_2000_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 66                 GJOG MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 67       GOLD_X_2009_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 68          GOLD_X_X_12 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 69                 GORT MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 70          HRUN_X_X_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 71       HSTA_X_2011_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 72                 HUTU MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 73       JADE_X_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 74                 JAMA MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 75       KALD_X_2010_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 76       KFSY_X_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 77       KODK_X_2004_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 78       LAMH_X_2001_09 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 79       LANO_X_2001_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 80      LAUR_X_1993_9_5 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 81   LITC_0_05_2008_841 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 82   LITC_0_05_2008_842 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 83    LITC_0_05_2008_FL MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 84    LITC_0_05_2008_FO MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 85   LITC_0_45_2008_789 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 86  LITC_23_32_2008_306 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 87  LITC_23_32_2008_324 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 88  LITC_23_32_2008_347 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 89  LITC_23_32_2008_356 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 90  LITC_23_32_2008_744 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 91       LLYD_X_2003_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 92          LMCK_X_X_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 93          LMIA_X_X_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 94       LMOR_X_2001_12 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 95       LNEA_M_2001_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 96       LNGH_X_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 97       LOBG_X_1999_09 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 98       LOBG_X_1999_11 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 99       LOBG_X_1999_12 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 100      LOBG_X_1999_13 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 101      LOBG_X_1999_32 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 102      LOBG_X_1999_36 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 103      LOBG_X_1999_38 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 104      LOBG_X_1999_39 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 105      LOBG_X_1999_43 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 106      LOBG_X_1999_46 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 107      LOBG_X_2012_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 108      LOBG_X_2012_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 109      LOBG_X_2012_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 110      LOBG_X_2012_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 111      LOBG_X_2012_06 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 112      LOBG_X_2012_08 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 113      LOBG_X_2012_11 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 114      LOBG_X_2012_17 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 115      LOBG_X_2012_26 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 116      LOBG_X_2012_28 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 117      LONG_X_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 118      LSHP_X_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 119      LSOL_X_2012_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 120      LSWL_X_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 121      LTLT_X_2011_06 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 122    LUTE_X_2003_76_4 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 123         MANC_X_X_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 124                MATA MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 125      MAYR_X_2009_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 126      MAYR_X_2009_11 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 127      MAYR_X_2004_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 128      MAYR_X_2004_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 129      MAYR_X_2004_09 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 130      MAYR_X_2004_13 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 131      MAYR_X_2004_14 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 132      MAYR_X_2004_17 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 133      MAYR_X_2004_21 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 134      MAYR_X_2004_24 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 135      MAYR_X_2004_26 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 136      MAYR_X_2004_30 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 137      MDPC_X_1993_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 138   MIDF_BDVW_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 139   MIDF_BDVW_2011_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 140   MIDF_BLUP_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 141   MIDF_REND_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 142   MIDF_REND_2011_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 143   MIDF_REND_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 144   MIDF_REND_2011_06 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 145   MIDF_REND_2011_10 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 146   MIDF_S101_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 147   MIDF_S101_2011_06 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 148         MNKA_X_X_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 149      MNYN_X_X_29997 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 150                MUDL MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 151                 NEU MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 152      NHBR_X_2003_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 153                NOST MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 154         NTRW_X_X_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 155      OBSE_X_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 156      OLNY_X_2007_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 157      ORPH_X_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 158                PAXB MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 159         PINC_X_X_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 160   POQU_X_2009_29995 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 161      QUIN_X_2003_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 162                RABS MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 163      RCAL_X_2001_24 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 164      RDSP_X_2010_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 165   RDSP_X_2012_70307 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 166   RDSP_X_2012_70311 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 167   RDSP_X_2012_70314 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 168   RDSP_X_2012_70332 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 169   RDSP_X_2012_70337 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 170   RDSP_X_2012_70346 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 171   RDSP_X_2012_70353 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 172   RDSP_X_2012_70364 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 173   RDSP_X_2012_70368 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 174   RDSP_X_2012_70385 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 175      REIV_X_2011_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 176      RGLN_X_2011_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 177     ROUG_X_2000_f03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 178    SACK_X_2010_0898 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 179                SALR MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 180         SALS_X_X_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 181         SAPC_X_X_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 182     SCRM_X_2010_873 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 183    SCRS_X_2009_8253 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 184                 SCX MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 185      SDPY_X_2006_24 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 186                SHEL MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 187      SHEL_L_2008_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 188    SJCR_X_2009_8212 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 189      SKID_X_2009_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 190         SKON_X_X_12 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 191    SLMW_X_2001_0918 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 192      SLTC_X_X_90458 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 193   SLVR_X_2009_29996 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 194      SPNC_L_2009_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 195      SPNC_L_2009_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 196      SPNC_O_2010_08 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 197      SPNC_O_2010_14 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 198      SRLY_X_2011_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 199     SRST_S1_2000_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 200      SSMC_X_2010_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 201      STIU_X_2009_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 202      STMY_X_2011_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 203         SUNC_X_X_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 204      TERN_X_2011_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 205      TORM_X_2011_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 206              TYNE_1 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 207      TYNE_1_2001_07 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 208      TYNE_1_2001_08 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 209      TYNE_1_2001_09 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 210      TYNE_1_2001_10 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 211      TYNE_1_2001_14 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 212              TYNE_8 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 213     TYNE_8_2003_902 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 214     TYNE_8_2003_906 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 215     TYNE_8_2003_908 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 216     TYNE_8_2003_919 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 217     TYNE_8_2003_920 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 218         URRI_X_X_07 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 219         VIFC_X_X_07 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 220         VIFR_X_X_08 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 221      WALC_X_2005_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 222      WALR_X_2005_32 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 223      WATT_X_2009_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 224      WDPL_X_2009_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 225    WMSO_X_2002_bigf MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 226      WOLF_X_2011_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 227      ZERO_X_2011_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
##     numreads covbases coverage meandepth meanbaseq meanmapq acronym type
## 1        567     8397  78.2864  3.876380      27.7     46.2    AKMA real
## 2       2059    10201  95.1054 14.412500      27.4     51.8    AKST real
## 3       2171     9737  90.7794 15.194800      23.3     51.4    ANSR real
## 4        119     2695  25.1259  0.394089      30.1     43.5    ANTL real
## 5        587     7844  73.1307  4.013980      27.0     47.6    BARW real
## 6        221     3613  33.6845  0.730934      29.9     45.2    BDGB real
## 7        594     5918  55.1743  1.974730      33.1     48.0    BEPA real
## 8        620     8482  79.0789  4.306270      27.4     47.0    BHAR real
## 9        706     5604  52.2469  2.359410      30.5     48.9    BIGL real
## 10       523     5326  49.6550  1.741560      31.2     49.2    BIGR real
## 11       553     7912  73.7647  3.648330      21.6     46.7    BIGR real
## 12       971     8886  82.8454  6.509510      21.4     45.9    BIGR real
## 13      1032     8865  82.6496  7.124000      27.0     49.7    BIGR real
## 14       754     8876  82.7522  5.148700      26.1     48.4    BIGR real
## 15      1011     8529  79.5171  6.987600      27.0     48.9    BIGR real
## 16      1634     9201  85.7822 11.253800      26.9     50.7    BIGR real
## 17      1057     8997  83.8803  7.211080      26.1     49.2    BIGR real
## 18      1222     9065  84.5143  8.391200      26.2     50.3    BIGR real
## 19      1445     8993  83.8430  9.992910      26.9     49.1    BIGR real
## 20      1019     8866  82.6590  6.969700      26.7     50.8    BIGR real
## 21      1059     8436  78.6500  7.282490      26.3     49.1    BITJ real
## 22       324     7743  72.1891  2.151030      22.6     46.9    BK70 real
## 23      1782     9830  91.6465 12.451600      23.0     51.0    BKW2 real
## 24      2797    10047  93.6696 19.518800      27.6     53.0    BLAU real
## 25       575     8523  79.4611  3.958230      27.8     47.7    BNMA real
## 26       951     9828  91.6278  6.660080      27.4     49.9    BNMA real
## 27       690     8638  80.5333  4.793490      27.5     49.3    BNMA real
## 28       476     8092  75.4428  3.286410      27.4     47.7    BNMA real
## 29       514     7970  74.3054  3.520600      27.4     48.0    BNMA real
## 30      1168     9970  92.9517  8.158310      26.6     52.3    BNST real
## 31      1073    10021  93.4272  7.537670      26.8     52.6    BNST real
## 32      1108     9847  91.8050  7.776150      26.7     51.9    BNST real
## 33       975     9607  89.5674  6.808410      26.9     52.1    BNST real
## 34       881     8900  82.9759  6.045030      26.9     49.8    BNST real
## 35      1674     9765  91.0405 11.714600      27.7     52.7    BOOT real
## 36      2238     9804  91.4041 15.621200      24.2     50.9    BOUL real
## 37      1895     9863  91.9541 13.228000      23.9     51.1    BOUL real
## 38      1916     9856  91.8889 13.280600      26.1     52.2    BRLY real
## 39      1950     9872  92.0380 13.632900      24.0     51.6    BRNT real
## 40       647     7433  69.2989  4.391390      27.9     48.6    BSEA real
## 41      1301     9011  84.0108  8.970170      26.2     49.7    CERC real
## 42      1131     9702  90.4531  7.903690      27.1     52.5    CHRU real
## 43      1499     9813  91.4880 10.449900      27.9     52.7    CMCB real
## 44       596     9189  85.6703  4.152340      27.6     51.7    COAT real
## 45      1414     9532  88.8682  9.785570      25.4     51.9    COND real
## 46      1754     9693  90.3692 12.248600      28.0     52.9    CORC real
## 47      1219    10002  93.2500  8.508020      27.5     52.9    DAIM real
## 48      1535     9863  91.9541 10.739200      27.8     52.5    DANS real
## 49      1033     8658  80.7197  7.135740      23.8     45.1    DARW real
## 50      1160     8935  83.3023  7.978000      23.6     46.0    DAWS real
## 51      1773     9937  92.6440 12.422000      27.7     52.4    DNSE real
## 52      2614     9872  92.0380 18.237000      23.5     51.2    DRIZ real
## 53      2752    10064  93.8281 19.223700      24.1     51.9    DRIZ real
## 54      4166    10206  95.1520 29.156200      23.7     51.0    DRIZ real
## 55      2731     9915  92.4389 19.051000      23.5     51.1    DRIZ real
## 56      2313    10179  94.9002 16.210800      27.7     52.3    ECHO real
## 57       969     9320  86.8917  6.726650      24.0     50.7    EDEN real
## 58      1293     8508  79.3213  8.877490      26.2     50.8    ERBC real
## 59      1514     9053  84.4024 10.440900      24.7     54.2    ESCP real
## 60      1050     9053  84.4024  7.270180      23.3     44.5    FADA real
## 61      1950     9238  86.1272 13.458100      21.9     49.1    FRIC real
## 62      1259     8728  81.3724  8.610010      24.9     51.1    FRIL real
## 63      1579     6514  60.7309  5.266920      29.5     49.6     FTC real
## 64      1318     8707  81.1766  9.043260      26.1     49.9    GARC real
## 65       599     8394  78.2584  4.097050      23.2     47.1    GIFU real
## 66       291     4057  37.8240  0.965691      30.1     44.4    GJOG real
## 67      3506     9983  93.0729 24.463700      23.3     51.1    GOLD real
## 68      1030     9935  92.6254  7.218530      27.3     53.4    GOLD real
## 69       266     4124  38.4486  0.885978      30.8     45.0    GORT real
## 70      2537    10058  93.7721 17.686900      26.7     51.9    HRUN real
## 71       602     8702  81.1300  4.134530      27.3     48.7    HSTA real
## 72      1206     6451  60.1436  4.023030      27.7     48.9    HUTU real
## 73      1927     9967  92.9237 13.518600      27.9     52.7    JADE real
## 74       326     4046  37.7214  1.080550      30.0     46.1    JAMA real
## 75       566     8454  78.8178  3.857080      27.2     48.2    KALD real
## 76      1870     9956  92.8212 13.130500      28.0     52.5    KFSY real
## 77       647     8310  77.4753  4.415810      26.9     46.6    KODK real
## 78       584     8381  78.1372  4.054630      26.8     49.4    LAMH real
## 79       684     8500  79.2467  4.714340      26.5     46.4    LANO real
## 80      1969     9309  86.7891 13.487400      24.9     51.8    LAUR real
## 81       585     8827  82.2954  3.995250      22.7     47.2    LITC real
## 82       588     8339  77.7457  3.988160      21.8     44.4    LITC real
## 83       348     6862  63.9754  2.350830      22.6     46.8    LITC real
## 84       602     7902  73.6715  3.995710      21.9     46.3    LITC real
## 85       862     8880  82.7895  5.966620      23.2     47.2    LITC real
## 86      1571     9717  90.5930 10.735900      22.2     50.7    LITC real
## 87      1250     9496  88.5325  8.629870      22.0     50.3    LITC real
## 88      1640     9480  88.3834 10.563800      21.5     48.4    LITC real
## 89      2083     9807  91.4320 14.445600      22.8     50.9    LITC real
## 90      1185     9434  87.9545  8.010630      22.0     49.9    LITC real
## 91       669     8385  78.1745  4.643480      27.5     48.3    LLYD real
## 92      1831     9963  92.8864 12.765300      27.7     52.6    LMCK real
## 93      1361     9395  87.5909  9.462610      25.3     52.3    LMIA real
## 94       902     8787  81.9224  6.177610      27.1     47.6    LMOR real
## 95      2383     9986  93.1009 16.629100      26.6     52.5    LNEA real
## 96       735     9657  90.0336  5.145350      27.3     51.9    LNGH real
## 97      1322     9668  90.1361  9.233920      27.4     50.5    LOBG real
## 98      1462     9641  89.8844 10.084300      26.2     51.5    LOBG real
## 99      2651     9809  91.4507 18.479500      26.2     52.4    LOBG real
## 100     1632     9701  90.4438 11.330200      26.3     51.3    LOBG real
## 101      803     8049  75.0420  5.517810      26.2     49.6    LOBG real
## 102     1363     9622  89.7073  9.395860      26.4     51.2    LOBG real
## 103     2276     9914  92.4296 15.827700      26.3     52.3    LOBG real
## 104     2308     9924  92.5228 16.054000      26.2     51.6    LOBG real
## 105     1297     9591  89.4182  8.998510      26.0     51.0    LOBG real
## 106      760     8791  81.9597  5.207720      26.7     47.7    LOBG real
## 107     1224     9712  90.5463  8.455900      26.4     51.8    LOBG real
## 108     1377     9839  91.7304  9.562190      26.3     51.9    LOBG real
## 109     1458     9990  93.1382 10.102000      26.5     50.7    LOBG real
## 110     1387     9952  92.7839  9.674340      26.4     50.4    LOBG real
## 111     1833    10084  94.0145 12.767300      26.8     52.0    LOBG real
## 112     1198     9585  89.3623  8.302260      26.7     50.7    LOBG real
## 113     1509     9686  90.3039 10.448400      26.5     51.0    LOBG real
## 114      831     8750  81.5775  5.728790      26.4     48.1    LOBG real
## 115     2061    10143  94.5646 14.336800      26.3     52.3    LOBG real
## 116     1950    10240  95.4690 13.624700      26.4     52.2    LOBG real
## 117     1863    10011  93.3340 13.025900      27.8     51.0    LONG real
## 118     1470    10006  93.2873 10.279000      27.8     52.8    LSHP real
## 119     1107     9052  84.3931  7.566100      24.9     49.8    LSOL real
## 120      563     8411  78.4169  3.827710      27.2     47.0    LSWL real
## 121      672     9024  84.1320  4.667350      27.0     45.9    LTLT real
## 122     1196     9530  88.8495  8.330690      26.2     52.3    LUTE real
## 123      745     8905  83.0226  5.144880      27.3     48.2    MANC real
## 124      343     4258  39.6979  1.142740      29.1     49.0    MATA real
## 125     2343     9963  92.8864 16.349200      23.9     50.6    MAYR real
## 126     2881     9767  91.0591 20.092600      23.3     51.4    MAYR real
## 127     2094     9728  90.6955 14.550800      25.7     53.0    MAYR real
## 128     2006     9744  90.8447 13.922200      25.7     53.1    MAYR real
## 129     1920     9908  92.3737 13.287600      25.9     52.4    MAYR real
## 130     1730     9948  92.7466 12.104500      26.8     52.1    MAYR real
## 131     2869     9597  89.4742 19.853000      24.7     54.0    MAYR real
## 132     3803     9387  87.5163 26.089000      24.0     54.6    MAYR real
## 133     2627     9888  92.1872 18.236200      25.6     53.5    MAYR real
## 134     1486     9651  89.9776 10.295800      25.7     52.7    MAYR real
## 135     2065     9640  89.8751 14.451900      25.5     51.9    MAYR real
## 136     2397     9546  88.9987 16.569100      25.0     53.6    MAYR real
## 137      831     8683  80.9528  5.717320      23.3     45.1    MDPC real
## 138     1207     9084  84.6914  8.274380      26.3     48.3    MIDF real
## 139      909     8716  81.2605  6.267670      26.1     48.8    MIDF real
## 140      936     8421  78.5102  6.429610      26.3     47.6    MIDF real
## 141     2220    10276  95.8046 15.502600      26.5     51.7    MIDF real
## 142     2175    10115  94.3036 15.172100      26.2     52.2    MIDF real
## 143     1794    10010  93.3246 12.447800      25.8     51.8    MIDF real
## 144     2221    10125  94.3968 15.385200      25.7     51.8    MIDF real
## 145     2308     9969  92.9424 16.083300      26.4     52.2    MIDF real
## 146     1181     8517  79.4052  8.056400      26.6     47.9    MIDF real
## 147      674     8799  82.0343  4.674720      26.3     47.6    MIDF real
## 148     1154     9851  91.8423  8.063680      27.6     51.9    MNKA real
## 149     1721     9926  92.5415 12.036500      27.7     51.7    MNYN real
## 150      831     6291  58.6519  2.758060      30.5     48.8    MUDL real
## 151      240      968   9.0248  0.801137      28.7     43.4     NEU real
## 152      680     8479  79.0509  4.662220      27.7     48.2    NHBR real
## 153      573     4571  42.6161  1.903970      29.8     46.4    NOST real
## 154      829     7241  67.5089  5.704270      25.9     45.2    NTRW real
## 155      548     8116  75.6666  3.804960      27.3     47.1    OBSE real
## 156      462     7475  69.6905  3.051460      20.4     47.1    OLNY real
## 157     1314     9906  92.3550  9.190010      27.6     51.8    ORPH real
## 158     1109     6343  59.1367  3.694010      29.6     49.4    PAXB real
## 159     1122     8821  82.2394  7.736900      26.3     50.8    PINC real
## 160      543     8364  77.9787  3.747530      27.2     47.3    POQU real
## 161      835     8873  82.7242  5.626980      20.2     51.6    QUIN real
## 162      372     4787  44.6299  1.621290      28.5     41.5    RABS real
## 163     1831     9710  90.5277 12.834600      26.6     52.0    RCAL real
## 164     2290     9955  92.8119 15.959500      23.4     50.3    RDSP real
## 165     2300     9885  92.1592 15.863100      26.5     51.9    RDSP real
## 166     1591     9532  88.8682 10.897800      26.1     53.0    RDSP real
## 167     1799     9999  93.2221 12.413900      26.6     52.2    RDSP real
## 168     1997     9473  88.3181 13.830500      26.4     52.8    RDSP real
## 169     1918     9890  92.2059 13.193100      26.1     52.2    RDSP real
## 170     1624     9714  90.5650 11.286700      26.4     52.5    RDSP real
## 171     1566     9684  90.2853 10.777600      26.4     52.3    RDSP real
## 172     1472     9383  87.4790 10.080000      26.0     53.4    RDSP real
## 173     1777     9798  91.3481 12.265800      26.2     52.8    RDSP real
## 174     1358     9569  89.2131  9.345610      26.3     51.8    RDSP real
## 175     1087     9517  88.7283  7.569640      26.7     50.6    REIV real
## 176     1168     9700  90.4345  8.196250      27.4     52.0    RGLN real
## 177     2332     9914  92.4296 16.129500      24.6     52.8    ROUG real
## 178     1452     8871  82.7056  9.953380      26.1     50.5    SACK real
## 179      151     3027  28.2211  0.499627      29.7     45.4    SALR real
## 180     1765     8993  83.8430 12.146600      25.8     50.9    SALS real
## 181     1087     8903  83.0039  7.464390      26.1     50.3    SAPC real
## 182     1269     8830  82.3233  8.721420      26.4     50.5    SCRM real
## 183     1392     8753  81.6054  9.640590      26.6     50.7    SCRS real
## 184      601     5994  55.8829  1.996080      30.8     49.5     SCX real
## 185     1177     9471  88.2995  8.165300      22.5     52.0    SDPY real
## 186      930     6015  56.0787  3.087640      30.7     50.1    SHEL real
## 187     1622     9173  85.5212 10.849000      20.9     49.1    SHEL real
## 188     1177     9260  86.3323  8.147680      26.6     49.0    SJCR real
## 189     2805    10083  94.0052 19.589300      23.3     50.7    SKID real
## 190     2011     9873  92.0474 14.053800      27.6     52.3    SKON real
## 191     1252     8415  78.4542  8.588480      23.9     52.1    SLMW real
## 192     2145    10039  93.5950 15.029900      27.8     51.7    SLTC real
## 193     1192     9621  89.6979  8.332840      26.8     53.5    SLVR real
## 194     2045     9969  92.9424 14.202900      23.4     49.8    SPNC real
## 195     1031     8624  80.4028  7.125210      23.3     46.8    SPNC real
## 196     2500     9852  91.8516 17.480000      23.2     51.5    SPNC real
## 197     3269     9929  92.5695 22.779700      23.2     51.4    SPNC real
## 198     1709    10051  93.7069 11.925900      27.7     52.3    SRLY real
## 199     1494     9507  88.6351 10.481700      26.3     52.3    SRST real
## 200     1467     9016  84.0574  9.990300      25.4     50.2    SSMC real
## 201     3015    10235  95.4223 21.003700      23.6     51.8    STIU real
## 202     1917    10116  94.3129 13.453800      27.7     52.4    STMY real
## 203     1206     9086  84.7101  8.258530      26.0     50.8    SUNC real
## 204     1699     9821  91.5626 11.876200      27.8     52.6    TERN real
## 205      721     8886  82.8454  4.968950      27.1     47.4    TORM real
## 206      306     4694  43.7628  1.015850      29.3     49.8    TYNE real
## 207     1029     8701  81.1206  7.162320      23.3     45.9    TYNE real
## 208     1032     8362  77.9601  7.149260      22.9     46.1    TYNE real
## 209     1040     8869  82.6869  7.154480      23.3     46.0    TYNE real
## 210     1610     9649  89.9590 11.176200      23.2     50.4    TYNE real
## 211     1049     8391  78.2305  7.274380      23.3     46.6    TYNE real
## 212      876     6318  58.9036  2.918240      30.4     48.4    TYNE real
## 213     1767     9917  92.4576 12.290000      23.5     51.1    TYNE real
## 214     2974     9905  92.3457 20.756400      22.4     51.4    TYNE real
## 215     2334     9764  91.0311 16.267400      23.2     51.0    TYNE real
## 216     2191    10007  93.2967 15.238400      23.1     51.1    TYNE real
## 217     2139     9891  92.2152 14.920900      23.0     50.9    TYNE real
## 218     2066     9706  90.4904 14.412100      26.5     52.4    URRI real
## 219     1988     9841  91.7490 13.873300      26.9     52.4    VIFC real
## 220     2697     9537  88.9148 18.640300      25.2     54.0    VIFR real
## 221     1715     9884  92.1499 11.986300      27.4     52.7    WALC real
## 222     1423     9689  90.3319  9.987320      27.3     52.6    WALR real
## 223     1304     9268  86.4069  9.104610      23.5     51.4    WATT real
## 224     1366     9878  92.0940  9.557710      23.3     51.3    WDPL real
## 225      441     7512  70.0354  2.937350      22.2     45.0    WMSO real
## 226     1753     9849  91.8236 12.170800      27.6     52.6    WOLF real
## 227     2126    10062  93.8094 14.920100      28.1     52.1    ZERO real
##     weighted_mean_depth                                                   pop
## 1             5.6593572                                         Alaska Marine
## 2             6.1191022                                         Alaska Stream
## 3            10.2665175                               Anser Lake, Haida Gwaii
## 4             0.7332322               Antigonish Landing, Nova Scotia, Marine
## 5             5.7129707                                        Barrow, Alaska
## 6             1.4560270                                            Bodega Bay
## 7             1.2070651                                              Bear Paw
## 8             5.2068374      North Uist, Scotland, Andrew Maccoll 21 May 2011
## 9             2.3439186                                          Big Lake (F)
## 10            1.6050164                                         Big River (M)
## 11            7.4781709                                         Big River, CA
## 12            7.5244250                                         Big River, CA
## 13            5.1880784                                         Big River, CA
## 14            6.3998250                                         Big River, CA
## 15            5.1195717                                         Big River, CA
## 16            5.2521757                                         Big River, CA
## 17            5.0344703                                         Big River, CA
## 18            5.8887788                                         Big River, CA
## 19            5.7324977                                         Big River, CA
## 20            4.8591415                                         Big River, CA
## 21            6.8958966                                          Bitrufjordur
## 22            9.0072574                         Banks West, lake, Haida Gwaii
## 23            9.6392857                           Banks 70, lake, Haida Gwaii
## 24            5.7998707                               Blautaver Lake, Iceland
## 25            5.3101227                                        Bonsall marine
## 26            5.8571863                                        Bonsall marine
## 27            4.5056283                                        Bonsall marine
## 28            4.7503363                                        Bonsall marine
## 29            4.6754872                                        Bonsall marine
## 30            5.1243798                                        Bonsall stream
## 31            4.9778562                                        Bonsall stream
## 32            5.1286995                                        Bonsall stream
## 33            4.3786743                                        Bonsall stream
## 34            5.3279879                                        Bonsall stream
## 35            5.0370307                                     Boot Lake, Alaska
## 36           11.0161867                             Boulton Lake, haida Gwaii
## 37            9.3903520                             Boulton Lake, haida Gwaii
## 38            5.6745386                                           Barley Lake
## 39           10.2002365                              Branta Lake, Haida Gwaii
## 40            6.8064430                                            Bering Sea
## 41            5.6196985                    Cerrito Creek, Northern California
## 42            4.9029401  North Uist, Scotland CHRU Andrew Maccoll 20 May 2011
## 43            4.7270258                                        Community Club
## 44            5.1469960                              Coates Lake, Haida Gwaii
## 45            5.6082479                            Connor Creek D, Washington
## 46            5.6744946                                 Corcoran Lake, Alaska
## 47            5.2588930           North Uist, DAIM Andrew Maccoll 24 May 2011
## 48            4.6453401                                  Daniels Lake, Alaska
## 49            9.3617612                              Darwin Lake, Haida Gwaii
## 50           11.1274830                        Dawson Marine Pond, Haida Gwai
## 51            5.5763697                                   Denise Lake, Alaska
## 52           12.9269793                      Drizzle Lake, inlet, Haida Gwaii
## 53           11.4626779                             Drizzle Lake, Haida Gwaii
## 54           12.0242899                             Drizzle Lake, Haida Gwaii
## 55           11.0507904                     Drizzle Lake, outlet, Haida Gwaii
## 56            6.7741298                                     Echo Lake, Alaska
## 57           11.3075050                                Eden Lake, Haida Gwaii
## 58            6.1012959                               El Rosario Boca, Mexico
## 59            6.3509442                          Escarpment Lake, Haida Gwaii
## 60           11.1778262                                 North Uist, Loch Fada
## 61            9.6235900                                          Friant River
## 62            5.9892293                                          Friant River
## 63            2.3527355                           Fish Trap Creek, Washington
## 64            5.8876132                    Garrity Creek, Northern California
## 65            5.4648449                                       Japanese Marine
## 66            1.8685515                               Gjogur, Iceland, Marine
## 67           13.6788189                               Gold Creek, Haida Gwaii
## 68            4.9021005                               Gold Creek, Haida Gwaii
## 69            1.7040520                        Gorten Sands, Scotland, Marine
## 70            5.9692801                                        Hraun, Iceland
## 71            5.3297352 North Uist, Scotland HOSTA Andrew Maccoll 18 May 2011
## 72            2.9365968                    Humptulips, Washington, Freshwater
## 73            5.9535365                                     Jade Lake, Alaska
## 74            2.2288292                                       Japanese Marine
## 75            5.1999993                               Kaldback, Faroe Islands
## 76            5.4475475                                       Kalifonsky Lake
## 77            6.0437283                  Pacific Ocean offshore Kodiak Island
## 78            5.0899309                                        Loch a'Mhuilin
## 79            5.8646859                                      Loch an Nostarie
## 80            8.4144698                              Laurel Pond, Haida Gwaii
## 81            7.4768327                            Little Campbell downstream
## 82            8.4862530                            Little Campbell downstream
## 83            7.1240731                            Little Campbell downstream
## 84            8.3245718                            Little Campbell downstream
## 85            9.2334751                            Little Campbell downstream
## 86            8.8145202                              Little Campbell upstream
## 87            8.7778775                              Little Campbell upstream
## 88            9.8111686                              Little Campbell upstream
## 89           10.6394774                              Little Campbell upstream
## 90            7.5975163                              Little Campbell upstream
## 91            5.5302740                                  Lloyd State Park, MA
## 92            5.1824694                           Little Meadow Creek, Alaska
## 93            6.7022353                                          Limia, Spain
## 94            7.9151401                                            Loch Morar
## 95            5.3970335                                         Loch nan Eala
## 96            4.7596208                  Lough Neagh, Ballyronan Bay, Ireland
## 97            5.7292047                                    Loberg Lake, early
## 98            6.7115305                                    Loberg Lake, early
## 99            7.4320446                                    Loberg Lake, early
## 100           7.3085139                                    Loberg Lake, early
## 101           7.6706016                                    Loberg Lake, early
## 102           6.2234395                                    Loberg Lake, early
## 103           6.6593630                                    Loberg Lake, early
## 104           7.0157263                                    Loberg Lake, early
## 105           5.9657157                                    Loberg Lake, early
## 106           6.8911003                                    Loberg Lake, early
## 107           5.8502730                                    Loberg Lake, later
## 108           6.1697366                                    Loberg Lake, later
## 109           6.0957819                                    Loberg Lake, later
## 110           6.1045093                                    Loberg Lake, later
## 111           5.5668464                                    Loberg Lake, later
## 112           5.7840358                                    Loberg Lake, later
## 113           6.8838001                                    Loberg Lake, later
## 114           7.1986307                                    Loberg Lake, later
## 115           5.9638877                                    Loberg Lake, later
## 116           5.5151988                                    Loberg Lake, later
## 117           5.9466847                                     Long Lake, Alaska
## 118           5.3319020                                         L-shaped lake
## 119           6.7036664                                       Lake Solano, CA
## 120           4.9910335                              Lough Swilly, Co Donegal
## 121           5.7242339                                  Lough Talt, Co Sligo
## 122           6.0352348                               Lutea Lake, Haida Gwaii
## 123           6.4361687                      Manchester Clam Bay, Puget Sound
## 124           2.0881693                                              Matadero
## 125          11.8436738                                            Mayer Lake
## 126           8.2861903                                            Mayer Lake
## 127           5.9841121                                            Mayer Lake
## 128           6.8030007                                            Mayer Lake
## 129           5.6622857                                            Mayer Lake
## 130           5.0628956                                            Mayer Lake
## 131           7.8243280                                            Mayer Lake
## 132           9.0175331                                            Mayer Lake
## 133           7.3820319                                            Mayer Lake
## 134           6.2882460                                            Mayer Lake
## 135           6.9276230                                            Mayer Lake
## 136           8.0912364                                            Mayer Lake
## 137          10.3976967                          Mid-pacific, off Haida Gwaii
## 138           6.9000706                          Midfjardara River Downstream
## 139           5.5948720                          Midfjardara River Downstream
## 140           6.1825375                          Midfjardara River Downstream
## 141           7.3160002                            Midfjardara River Upstream
## 142           5.3980437                            Midfjardara River Upstream
## 143           6.2871038                            Midfjardara River Upstream
## 144           6.8262899                            Midfjardara River Upstream
## 145           6.4462492                            Midfjardara River Upstream
## 146           7.1926416                          Midfjardara River Downstream
## 147           5.8657823                          Midfjardara River Downstream
## 148           5.1867059                                Matanuska Lake, Alaska
## 149           5.2552549                           Menyanthes Lake, Haida Gwai
## 150           1.4220406                                              Mud Lake
## 151           1.5902901                             Neustadt, Germany, Marine
## 152           6.0468999                       New Harbor River, US East Coast
## 153           0.8447451                             Norway Stream, Freshwater
## 154           6.7714109                                        Norway Trawler
## 155           5.5536763                    Scotland, OBSE+OBSM Andrew Maccoll
## 156           8.3406836                               Olney Creek, California
## 157           4.5714907                                   Orphea Lake, Alaska
## 158           1.9925720                                        Paxton Benthic
## 159           5.0384202                     Pinole Creek, Northern California
## 160           5.1586238                               Poque Lake, Haida Gwaii
## 161           6.7023087                                   Quinalt, Washington
## 162           3.0829753                                         Rabbit Slough
## 163           5.8027280                                River Callop, Scotland
## 164          11.0519227                                         Roadside Pond
## 165           7.6260500                                         Roadside Pond
## 166           6.3088523                                         Roadside Pond
## 167           5.9678947                                         Roadside Pond
## 168           6.6826979                                         Roadside Pond
## 169           6.9902077                                         Roadside Pond
## 170           5.6068552                                         Roadside Pond
## 171           6.2901291                                         Roadside Pond
## 172           5.0363602                                         Roadside Pond
## 173           6.8767427                                         Roadside Pond
## 174           7.1022094                                         Roadside Pond
## 175           5.1747957                  North Uist, Scotland, Andrew Maccoll
## 176           5.3614152                     River Glenavy, Co Antrim, Ireland
## 177           7.2687331                               Rouge Lake, Haida Gwaii
## 178           5.8404062                           San Antonio Creek, VAFB, CA
## 179           1.1687793                                  Salmon River, marine
## 180           6.6431733                                     Salinas River, CA
## 181           4.9594245                  San Pablo Creek, Northern California
## 182           6.0176383                       Santa Clara River mouth, LA, CA
## 183           6.5637238                             Santa Clara River, LA, CA
## 184           1.1804410                   Schwalle River, Germany, freshwater
## 185          11.7550906                         Serendipity Pond, Haida Gwaii
## 186           1.5803198                     River Shiel, Scotland, freshwater
## 187           7.6669384                                            Loch Shiel
## 188           5.8217646                  San Jacinto River, San Bernadino, CA
## 189           9.3390974                            Skidgate Lake, Haida Gwaii
## 190           6.2545067                              Skonun Lake, Haida Gwaii
## 191           5.7520814                   Sugarloaf Meadow, San Bernadino, CA
## 192           6.1719665                            Solstice Lake, Haida Gwaii
## 193           5.4704310                              Silver Lake, Haida Gwaii
## 194          10.4703091                              Spence Lake, Haida Gwaii
## 195          10.8371614                              Spence Lake, Haida Gwaii
## 196          10.7987807                       Spence Lake Outlet, Haida Gwaii
## 197          11.0222917                       Spence Lake Outlet, Haida Gwaii
## 198           5.1617288                              South Rolly Lake, Alaska
## 199           5.5126936                 Salmon River Stream, British Columbia
## 200           6.8748735                                  San Simeon Creek, CA
## 201           9.8822717      Stiu Lake, Queen Charlotte - fully armored fresh
## 202           5.6529617                                   Stormy Lake, Alaska
## 203           5.2009857                     Suisun Creek, Northern California
## 204           5.2308375                                     Tern Lake, Alaska
## 205           6.4907516                                   Torm Lake, Scotland
## 206           0.9806016                                       Tyne downstream
## 207          10.3758825                                     Tyne River marine
## 208          10.2345778                                     Tyne River marine
## 209          10.1085230                                     Tyne River marine
## 210           8.0013988                                     Tyne River marine
## 211          10.6449995                                     Tyne River marine
## 212           2.2853489                                         Tyne upstream
## 213           8.5327233                                   Tyne River upstream
## 214          14.3031165                                   Tyne River upstream
## 215          10.8699134                                   Tyne River upstream
## 216          10.1857972                                   Tyne River upstream
## 217          10.2538999                                   Tyne River upstream
## 218           6.3337425                                        Urridakotsvatn
## 219           5.8010832                                        Vifissta_avatn
## 220           7.8636075                                        Vifissta_avatn
## 221           6.2753807                                          Wallace Lake
## 222           5.7690872                                          Wallace Lake
## 223           6.6066058                                Watt Lake, Haida Gwaii
## 224           5.2269304                            Woodpile Creek, Haida gwai
## 225           7.1172362                            Williamsoni, CA; no plates
## 226           5.5945258                                     Wolf Lake, Alaska
## 227           4.9839896                                     Zero Lake, Alaska
##     coord_approx GPS_north GPS_east mar_fresh             notes      water_type
## 1           <NA>    60.124 -149.395         M              <NA>          Marine
## 2           <NA>    60.141 -149.395         F              <NA>           River
## 3           <NA>    54.114 -131.686         F              <NA>      Freshwater
## 4           <NA>    45.698  -61.878         M Jones et al. 2012          Marine
## 5           <NA>    71.335 -156.606         M              <NA>          Marine
## 6           <NA>    38.325 -123.041         M Jones et al. 2012          Marine
## 7           <NA>    61.615 -149.757         F Jones et al. 2012           Fresh
## 8           <NA>    57.567   -7.283         F              <NA>            Lake
## 9           <NA>    39.300 -123.728         F Jones et al. 2012           Fresh
## 10          <NA>    39.289 -123.747         M Jones et al. 2012          Marine
## 11          <NA>    39.289 -123.747         M              <NA>          Marine
## 12          <NA>    39.317 -123.686         F              <NA>           River
## 13          <NA>    39.289 -123.747         M              <NA>          Marine
## 14          <NA>    39.289 -123.747         M              <NA>          Marine
## 15          <NA>    39.289 -123.747         M              <NA>          Marine
## 16          <NA>    39.289 -123.747         M              <NA>          Marine
## 17          <NA>    39.317 -123.686         F              <NA>           River
## 18          <NA>    39.317 -123.686         F              <NA>           River
## 19          <NA>    39.317 -123.686         F              <NA>           River
## 20          <NA>    39.317 -123.686         F              <NA>           River
## 21          <NA>    65.457  -21.440         M              <NA>          Marine
## 22          <NA>    53.397 -130.202         F              <NA>      Freshwater
## 23          <NA>    53.359 -130.157         F              <NA>      Freshwater
## 24          <NA>    64.044  -18.991         F              <NA>            Lake
## 25          <NA>    48.885 -123.667         M              <NA>          Marine
## 26          <NA>    48.885 -123.667         M              <NA>          Marine
## 27          <NA>    48.885 -123.667         M              <NA>          Marine
## 28          <NA>    48.885 -123.667         M              <NA>          Marine
## 29          <NA>    48.885 -123.667         M              <NA>          Marine
## 30          <NA>    48.850 -123.723         F              <NA>           River
## 31          <NA>    48.850 -123.723         F              <NA>           River
## 32          <NA>    48.850 -123.723         F              <NA>           River
## 33          <NA>    48.850 -123.723         F              <NA>           River
## 34          <NA>    48.850 -123.723         F              <NA>           River
## 35          <NA>    61.718 -150.130         F              <NA>            Lake
## 36          <NA>    53.783 -132.098         F              <NA>            Lake
## 37          <NA>    53.783 -132.098         F              <NA>            Lake
## 38          <NA>    61.363 -150.083         F              <NA>            Lake
## 39          <NA>    53.967 -132.016         F              <NA>      Freshwater
## 40             Y    58.089 -166.643         M              <NA>          Marine
## 41          <NA>    37.901 -122.281         F              <NA>      Freshwater
## 42          <NA>    57.600   -7.200         F              <NA>           Fresh
## 43          <NA>    60.702 -151.383         F              <NA>           Fresh
## 44          <NA>    53.669 -132.880         F              <NA>           Fresh
## 45          <NA>    47.056 -124.163         F              <NA>           River
## 46          <NA>    61.574 -149.688         F              <NA>            Lake
## 47          <NA>    57.583   -7.200         F              <NA>           Fresh
## 48          <NA>    60.735 -151.186         F              <NA>            Lake
## 49          <NA>    52.568 -131.663         F              <NA>            Lake
## 50          <NA>    53.225 -132.476         M              <NA>          Marine
## 51          <NA>    60.522 -150.987         F              <NA>            Lake
## 52          <NA>    53.925 -132.077         F              <NA>            Lake
## 53          <NA>    53.935 -132.073         F              <NA>            Lake
## 54          <NA>    53.935 -132.073         F              <NA>            Lake
## 55          <NA>    53.934 -132.053         F              <NA>            Lake
## 56          <NA>    60.438 -151.161         F              <NA>            Lake
## 57          <NA>    53.845 -132.746         F              <NA>            Lake
## 58             Y    30.036 -115.774         F              <NA>            <NA>
## 59          <NA>    52.589 -131.842         F              <NA>            Lake
## 60          <NA>    57.613   -7.211         F              <NA>            Lake
## 61          <NA>    36.980 -119.731         F Completely plated           River
## 62          <NA>    36.980 -119.731         F        Low plated           River
## 63          <NA>    48.931 -122.487         F Jones et al. 2012           Fresh
## 64          <NA>    38.001 -122.322         F              <NA>           Creek
## 65             Y    35.405  136.701         M              <NA>          Marine
## 66          <NA>    65.980  -21.440         M Jones et al. 2012          Marine
## 67          <NA>    53.632 -132.053         F              <NA>           Fresh
## 68          <NA>    53.632 -132.053         F              <NA>           Fresh
## 69          <NA>    56.911   -5.888         M Jones et al. 2012          Marine
## 70          <NA>    64.917  -22.167         F              <NA>            <NA>
## 71          <NA>    57.617   -7.483         F              <NA>           fresh
## 72          <NA>    47.231 -123.957         F Jones et al. 2012           Fresh
## 73          <NA>    61.524 -149.869         F              <NA>            Lake
## 74          <NA>    42.973  144.329         M Jones et al. 2012          Marine
## 75          <NA>    62.064   -6.913         M              <NA>          Marine
## 76          <NA>    60.331 -151.264         F              <NA>            Lake
## 77             Y    56.965 -151.350         M              <NA>          Marine
## 78          <NA>    56.894   -5.869         F              <NA>            Lake
## 79          <NA>    56.993   -5.804         F              <NA>            Lake
## 80          <NA>    53.929 -132.020         F              <NA>            Lake
## 81          <NA>    49.013 -122.779         M              <NA>          Marine
## 82          <NA>    49.013 -122.779         M              <NA>          Marine
## 83          <NA>    49.013 -122.779         M              <NA>          Marine
## 84          <NA>    49.013 -122.779         M              <NA>          Marine
## 85          <NA>    49.013 -122.779         M              <NA>          Marine
## 86          <NA>    49.012 -122.625         F              <NA>           River
## 87          <NA>    49.012 -122.625         F              <NA>           River
## 88          <NA>    49.012 -122.625         F              <NA>           River
## 89          <NA>    49.012 -122.625         F              <NA>           River
## 90          <NA>    49.012 -122.625         F              <NA>           River
## 91          <NA>    41.530  -70.981         M              <NA>          Marine
## 92          <NA>    61.569 -149.761         F              <NA>           River
## 93          <NA>    41.910   -8.093         F              <NA>           River
## 94          <NA>    57.567   -7.267         F              <NA>            Lake
## 95          <NA>    56.906   -5.833         F              <NA>            Lake
## 96          <NA>    54.708   -6.528         F              <NA> Very Large Lake
## 97          <NA>    61.560 -149.258         F              <NA>            Lake
## 98          <NA>    61.560 -149.258         F              <NA>            Lake
## 99          <NA>    61.560 -149.258         F              <NA>            Lake
## 100         <NA>    61.560 -149.258         F              <NA>            Lake
## 101         <NA>    61.560 -149.258         F              <NA>            Lake
## 102         <NA>    61.560 -149.258         F              <NA>            Lake
## 103         <NA>    61.560 -149.258         F              <NA>            Lake
## 104         <NA>    61.560 -149.258         F              <NA>            Lake
## 105         <NA>    61.560 -149.258         F              <NA>            Lake
## 106         <NA>    61.560 -149.258         F              <NA>            Lake
## 107         <NA>    61.560 -149.258         F              <NA>            Lake
## 108         <NA>    61.560 -149.258         F              <NA>            Lake
## 109         <NA>    61.560 -149.258         F              <NA>            Lake
## 110         <NA>    61.560 -149.258         F              <NA>            Lake
## 111         <NA>    61.560 -149.258         F              <NA>            Lake
## 112         <NA>    61.560 -149.258         F              <NA>            Lake
## 113         <NA>    61.560 -149.258         F              <NA>            Lake
## 114         <NA>    61.560 -149.258         F              <NA>            Lake
## 115         <NA>    61.560 -149.258         F              <NA>            Lake
## 116         <NA>    61.560 -149.258         F              <NA>            Lake
## 117         <NA>    61.578 -149.764         F              <NA>            Lake
## 118         <NA>    61.706 -149.972         F              <NA>            Lake
## 119         <NA>    38.495 -122.033         F              <NA>            Lake
## 120         <NA>    55.016   -7.573         M              <NA>          Marine
## 121         <NA>    54.082   -8.920         F              <NA>            Lake
## 122         <NA>    52.337 -131.370         F              <NA>            Lake
## 123         <NA>    47.567 -122.547         M              <NA>          Marine
## 124         <NA>    37.393 -122.162         F Jones et al. 2012           Fresh
## 125         <NA>    53.692 -132.044         F              <NA>            Lake
## 126         <NA>    53.692 -132.044         F              <NA>            Lake
## 127         <NA>    53.692 -132.044         F              <NA>            Lake
## 128         <NA>    53.692 -132.044         F              <NA>            Lake
## 129         <NA>    53.692 -132.044         F              <NA>            Lake
## 130         <NA>    53.692 -132.044         F              <NA>            Lake
## 131         <NA>    53.692 -132.044         F              <NA>            Lake
## 132         <NA>    53.692 -132.044         F              <NA>            Lake
## 133         <NA>    53.692 -132.044         F              <NA>            Lake
## 134         <NA>    53.692 -132.044         F              <NA>            Lake
## 135         <NA>    53.692 -132.044         F              <NA>            Lake
## 136         <NA>    53.692 -132.044         F              <NA>            Lake
## 137            Y    53.000 -133.000         M              <NA>          Marine
## 138         <NA>    65.346  -20.911         M              <NA>          Marine
## 139         <NA>    65.346  -20.911         M              <NA>          Marine
## 140         <NA>    65.346  -20.911         M              <NA>          Marine
## 141         <NA>    65.037  -20.714         F              <NA>           River
## 142         <NA>    65.037  -20.714         F              <NA>           River
## 143         <NA>    65.037  -20.714         F              <NA>           River
## 144         <NA>    65.037  -20.714         F              <NA>           River
## 145         <NA>    65.037  -20.714         F              <NA>           River
## 146         <NA>    65.346  -20.911         M              <NA>          Marine
## 147         <NA>    65.346  -20.911         M              <NA>          Marine
## 148         <NA>    61.556 -149.229         F              <NA>            Lake
## 149         <NA>    53.596 -132.971         F              <NA>            Lake
## 150         <NA>    61.593 -149.340         F Jones et al. 2012            Lake
## 151         <NA>    54.058   10.877         M Jones et al. 2012          Marine
## 152         <NA>    44.473  -64.082         M              <NA>          Marine
## 153         <NA>    59.765    5.712         F Jones et al. 2012           Fresh
## 154            Y    68.500    2.000         M              <NA>          Marine
## 155            Y    57.614   -7.179         F              <NA>            <NA>
## 156         <NA>    40.528 -122.384         F              <NA>           River
## 157         <NA>    60.388 -151.199         F              <NA>            Lake
## 158         <NA>    49.703 -124.522         F Jones et al. 2012           Fresh
## 159         <NA>    37.963 -122.202         F              <NA>           Creek
## 160         <NA>    52.602 -131.704         F              <NA>            Lake
## 161         <NA>    47.471 -123.871         F              <NA>           Fresh
## 162         <NA>    61.556 -149.249         M Jones et al. 2012          Marine
## 163         <NA>    56.867   -5.425         F              <NA>           River
## 164         <NA>    53.624 -132.036         F              <NA>            Lake
## 165         <NA>    53.624 -132.036         F              <NA>            Lake
## 166         <NA>    53.624 -132.036         F              <NA>            Lake
## 167         <NA>    53.624 -132.036         F              <NA>            Lake
## 168         <NA>    53.624 -132.036         F              <NA>            Lake
## 169         <NA>    53.624 -132.036         F              <NA>            Lake
## 170         <NA>    53.624 -132.036         F              <NA>            Lake
## 171         <NA>    53.624 -132.036         F              <NA>            Lake
## 172         <NA>    53.624 -132.036         F              <NA>            Lake
## 173         <NA>    53.624 -132.036         F              <NA>            Lake
## 174         <NA>    53.624 -132.036         F              <NA>            Lake
## 175         <NA>    57.617   -7.517         F              <NA>            Lake
## 176         <NA>    54.588   -6.239         F              <NA>           River
## 177         <NA>    54.034 -131.876         F              <NA>            Lake
## 178         <NA>    34.783 -120.536         F              <NA>           River
## 179         <NA>    49.175 -122.594         M Jones et al. 2012          Marine
## 180         <NA>    36.647 -121.702         F              <NA>           River
## 181         <NA>    37.966 -122.320         F              <NA>           Creek
## 182         <NA>    34.236 -119.257         M              <NA>          Marine
## 183            Y    34.436 -118.612         F              <NA>           Fresh
## 184         <NA>    54.080   10.083         F Jones et al. 2012           Fresh
## 185         <NA>    54.028 -131.761         F              <NA>           Fresh
## 186         <NA>    56.748   -5.698         F Jones et al. 2012           Fresh
## 187         <NA>    56.787   -5.604         F              <NA>            Lake
## 188            Y    33.765 -117.208         F              <NA>           River
## 189         <NA>    53.097 -131.916         F              <NA>            Lake
## 190         <NA>    53.914 -132.025         F              <NA>            Lake
## 191            Y    34.179 -116.830         F              <NA>           Fresh
## 192         <NA>    53.945 -131.932         F              <NA>            Lake
## 193         <NA>    54.103 -131.688         F              <NA>            Lake
## 194         <NA>    53.973 -131.780         F              <NA>            Lake
## 195         <NA>    53.973 -131.780         F              <NA>            Lake
## 196         <NA>    53.982 -131.790         F              <NA>            Lake
## 197         <NA>    53.982 -131.790         F              <NA>            Lake
## 198         <NA>    61.669 -150.126         F              <NA>            Lake
## 199         <NA>    49.175 -122.594         F              <NA>           River
## 200            Y    35.608 -121.091         F              <NA>           River
## 201         <NA>    53.244 -132.586         F              <NA>            Lake
## 202         <NA>    60.771 -151.047         F              <NA>            Lake
## 203            Y    38.225 -122.107         F              <NA>           Creek
## 204         <NA>    60.533 -149.550         F              <NA>            Lake
## 205         <NA>    57.550   -7.317         F              <NA>            Lake
## 206         <NA>    55.999   -2.520         M Jones et al. 2012          Marine
## 207         <NA>    55.999   -2.520         M              <NA>          Marine
## 208         <NA>    55.999   -2.520         M              <NA>          Marine
## 209         <NA>    55.999   -2.520         M              <NA>          Marine
## 210         <NA>    55.999   -2.520         M              <NA>          Marine
## 211         <NA>    55.999   -2.520         M              <NA>          Marine
## 212         <NA>    55.943   -2.785         F Jones et al. 2012           Fresh
## 213         <NA>    55.943   -2.785         F              <NA>           River
## 214         <NA>    55.943   -2.785         F              <NA>           River
## 215         <NA>    55.943   -2.785         F              <NA>           River
## 216         <NA>    55.943   -2.785         F              <NA>           River
## 217         <NA>    55.943   -2.785         F              <NA>           River
## 218         <NA>    64.157  -21.343         F              <NA>           Fresh
## 219         <NA>    64.080  -21.873         F   Pelvis Complete           Fresh
## 220         <NA>    64.080  -21.873         F    Pelvis Reduced           Fresh
## 221         <NA>    61.573 -149.576         F   Pelvis Complete            Lake
## 222         <NA>    61.573 -149.576         F    Pelvis Reduced            Lake
## 223         <NA>    53.764 -132.071         F              <NA>            Lake
## 224         <NA>    53.644 -132.082         F              <NA>            Lake
## 225         <NA>    34.435 -118.198         F              <NA>           Fresh
## 226         <NA>    61.645 -149.278         F              <NA>            Lake
## 227         <NA>    61.648 -149.808         F              <NA>            Lake
##     PNW_independent_MvsF_c150 NorthEurope_independent_MvsF_c151
## 1                           1                                NA
## 2                           0                                NA
## 3                           0                                NA
## 4                          NA                                NA
## 5                           1                                NA
## 6                          NA                                NA
## 7                           0                                NA
## 8                          NA                                NA
## 9                          NA                                NA
## 10                         NA                                NA
## 11                         NA                                NA
## 12                         NA                                NA
## 13                         NA                                NA
## 14                         NA                                NA
## 15                         NA                                NA
## 16                         NA                                NA
## 17                         NA                                NA
## 18                         NA                                NA
## 19                         NA                                NA
## 20                         NA                                NA
## 21                         NA                                 1
## 22                          0                                NA
## 23                          0                                NA
## 24                         NA                                 0
## 25                          1                                NA
## 26                         NA                                NA
## 27                         NA                                NA
## 28                         NA                                NA
## 29                         NA                                NA
## 30                          0                                NA
## 31                         NA                                NA
## 32                         NA                                NA
## 33                         NA                                NA
## 34                         NA                                NA
## 35                          0                                NA
## 36                          0                                NA
## 37                         NA                                NA
## 38                          0                                NA
## 39                          0                                NA
## 40                          1                                NA
## 41                         NA                                NA
## 42                         NA                                 0
## 43                          0                                NA
## 44                          0                                NA
## 45                          0                                NA
## 46                          0                                NA
## 47                         NA                                NA
## 48                          0                                NA
## 49                          0                                NA
## 50                          1                                NA
## 51                          0                                NA
## 52                         NA                                NA
## 53                          0                                NA
## 54                         NA                                NA
## 55                         NA                                NA
## 56                          0                                NA
## 57                          0                                NA
## 58                         NA                                NA
## 59                          0                                NA
## 60                         NA                                NA
## 61                         NA                                NA
## 62                         NA                                NA
## 63                          0                                NA
## 64                         NA                                NA
## 65                         NA                                NA
## 66                         NA                                 1
## 67                          0                                NA
## 68                         NA                                NA
## 69                         NA                                 1
## 70                         NA                                 0
## 71                         NA                                NA
## 72                          0                                NA
## 73                          0                                NA
## 74                         NA                                NA
## 75                         NA                                 1
## 76                          0                                NA
## 77                          1                                NA
## 78                         NA                                 0
## 79                         NA                                 0
## 80                          0                                NA
## 81                          1                                NA
## 82                         NA                                NA
## 83                         NA                                NA
## 84                         NA                                NA
## 85                         NA                                NA
## 86                          0                                NA
## 87                         NA                                NA
## 88                         NA                                NA
## 89                         NA                                NA
## 90                         NA                                NA
## 91                         NA                                NA
## 92                          0                                NA
## 93                         NA                                NA
## 94                         NA                                NA
## 95                         NA                                 0
## 96                         NA                                 0
## 97                         NA                                NA
## 98                         NA                                NA
## 99                         NA                                NA
## 100                        NA                                NA
## 101                        NA                                NA
## 102                        NA                                NA
## 103                        NA                                NA
## 104                        NA                                NA
## 105                        NA                                NA
## 106                        NA                                NA
## 107                        NA                                NA
## 108                        NA                                NA
## 109                        NA                                NA
## 110                        NA                                NA
## 111                        NA                                NA
## 112                        NA                                NA
## 113                        NA                                NA
## 114                        NA                                NA
## 115                        NA                                NA
## 116                        NA                                NA
## 117                         0                                NA
## 118                         0                                NA
## 119                        NA                                NA
## 120                        NA                                 1
## 121                        NA                                 0
## 122                         0                                NA
## 123                         1                                NA
## 124                        NA                                NA
## 125                         0                                NA
## 126                        NA                                NA
## 127                        NA                                NA
## 128                        NA                                NA
## 129                        NA                                NA
## 130                        NA                                NA
## 131                        NA                                NA
## 132                        NA                                NA
## 133                        NA                                NA
## 134                        NA                                NA
## 135                        NA                                NA
## 136                        NA                                NA
## 137                         1                                NA
## 138                        NA                                NA
## 139                        NA                                NA
## 140                        NA                                 1
## 141                        NA                                 0
## 142                        NA                                NA
## 143                        NA                                NA
## 144                        NA                                NA
## 145                        NA                                NA
## 146                        NA                                NA
## 147                        NA                                NA
## 148                         0                                NA
## 149                         0                                NA
## 150                         0                                NA
## 151                        NA                                 1
## 152                        NA                                NA
## 153                        NA                                 0
## 154                        NA                                 1
## 155                        NA                                NA
## 156                        NA                                NA
## 157                         0                                NA
## 158                         0                                NA
## 159                        NA                                NA
## 160                         0                                NA
## 161                         0                                NA
## 162                         1                                NA
## 163                        NA                                 0
## 164                        NA                                NA
## 165                        NA                                NA
## 166                        NA                                NA
## 167                        NA                                NA
## 168                        NA                                NA
## 169                        NA                                NA
## 170                        NA                                NA
## 171                        NA                                NA
## 172                        NA                                NA
## 173                        NA                                NA
## 174                        NA                                NA
## 175                        NA                                 0
## 176                        NA                                 0
## 177                         0                                NA
## 178                        NA                                NA
## 179                         1                                NA
## 180                        NA                                NA
## 181                        NA                                NA
## 182                        NA                                NA
## 183                        NA                                NA
## 184                        NA                                 0
## 185                         0                                NA
## 186                        NA                                NA
## 187                        NA                                 0
## 188                        NA                                NA
## 189                         0                                NA
## 190                         0                                NA
## 191                        NA                                NA
## 192                         0                                NA
## 193                         0                                NA
## 194                         0                                NA
## 195                        NA                                NA
## 196                        NA                                NA
## 197                        NA                                NA
## 198                         0                                NA
## 199                         0                                NA
## 200                        NA                                NA
## 201                         0                                NA
## 202                         0                                NA
## 203                        NA                                NA
## 204                         0                                NA
## 205                        NA                                NA
## 206                        NA                                NA
## 207                        NA                                NA
## 208                        NA                                NA
## 209                        NA                                NA
## 210                        NA                                NA
## 211                        NA                                 1
## 212                        NA                                NA
## 213                        NA                                 0
## 214                        NA                                NA
## 215                        NA                                NA
## 216                        NA                                NA
## 217                        NA                                NA
## 218                        NA                                 0
## 219                        NA                                NA
## 220                        NA                                 0
## 221                        NA                                NA
## 222                         0                                NA
## 223                         0                                NA
## 224                         0                                NA
## 225                        NA                                NA
## 226                         0                                NA
## 227                         0                                NA
##     CaliforniaFreshwater_vs_AllPacificMarine_c153 c154_globalsuperglacial_FvsM
## 1                                               1                            1
## 2                                              NA                           NA
## 3                                              NA                           NA
## 4                                              NA                            1
## 5                                               1                            1
## 6                                               1                           NA
## 7                                              NA                            0
## 8                                              NA                           NA
## 9                                              NA                           NA
## 10                                             NA                           NA
## 11                                              1                           NA
## 12                                              0                           NA
## 13                                             NA                           NA
## 14                                             NA                           NA
## 15                                             NA                           NA
## 16                                             NA                           NA
## 17                                             NA                           NA
## 18                                             NA                           NA
## 19                                             NA                           NA
## 20                                             NA                           NA
## 21                                             NA                            1
## 22                                             NA                           NA
## 23                                             NA                           NA
## 24                                             NA                            0
## 25                                              1                            1
## 26                                             NA                           NA
## 27                                             NA                           NA
## 28                                             NA                           NA
## 29                                             NA                           NA
## 30                                             NA                            0
## 31                                             NA                           NA
## 32                                             NA                           NA
## 33                                             NA                           NA
## 34                                             NA                           NA
## 35                                             NA                           NA
## 36                                             NA                            0
## 37                                             NA                           NA
## 38                                             NA                           NA
## 39                                             NA                            0
## 40                                              1                            1
## 41                                              0                           NA
## 42                                             NA                            0
## 43                                             NA                           NA
## 44                                             NA                           NA
## 45                                             NA                           NA
## 46                                             NA                           NA
## 47                                             NA                           NA
## 48                                             NA                           NA
## 49                                             NA                           NA
## 50                                              1                            1
## 51                                             NA                           NA
## 52                                             NA                           NA
## 53                                             NA                            0
## 54                                             NA                           NA
## 55                                             NA                           NA
## 56                                             NA                           NA
## 57                                             NA                           NA
## 58                                              0                           NA
## 59                                             NA                            0
## 60                                             NA                           NA
## 61                                             NA                           NA
## 62                                              0                           NA
## 63                                             NA                            0
## 64                                              0                           NA
## 65                                             NA                            1
## 66                                             NA                            1
## 67                                             NA                           NA
## 68                                             NA                           NA
## 69                                             NA                            1
## 70                                             NA                            0
## 71                                             NA                           NA
## 72                                             NA                           NA
## 73                                             NA                           NA
## 74                                             NA                            1
## 75                                             NA                            1
## 76                                             NA                            0
## 77                                              1                            1
## 78                                             NA                            0
## 79                                             NA                            0
## 80                                             NA                           NA
## 81                                              1                            1
## 82                                             NA                           NA
## 83                                             NA                           NA
## 84                                             NA                           NA
## 85                                             NA                           NA
## 86                                             NA                            0
## 87                                             NA                           NA
## 88                                             NA                           NA
## 89                                             NA                           NA
## 90                                             NA                           NA
## 91                                             NA                            1
## 92                                             NA                           NA
## 93                                             NA                           NA
## 94                                             NA                           NA
## 95                                             NA                            0
## 96                                             NA                            0
## 97                                             NA                           NA
## 98                                             NA                           NA
## 99                                             NA                           NA
## 100                                            NA                           NA
## 101                                            NA                           NA
## 102                                            NA                           NA
## 103                                            NA                           NA
## 104                                            NA                           NA
## 105                                            NA                           NA
## 106                                            NA                           NA
## 107                                            NA                           NA
## 108                                            NA                           NA
## 109                                            NA                           NA
## 110                                            NA                           NA
## 111                                            NA                           NA
## 112                                            NA                           NA
## 113                                            NA                           NA
## 114                                            NA                           NA
## 115                                            NA                           NA
## 116                                            NA                           NA
## 117                                            NA                           NA
## 118                                            NA                            0
## 119                                             0                           NA
## 120                                            NA                            1
## 121                                            NA                            0
## 122                                            NA                           NA
## 123                                             1                            1
## 124                                             0                           NA
## 125                                            NA                            0
## 126                                            NA                           NA
## 127                                            NA                           NA
## 128                                            NA                           NA
## 129                                            NA                           NA
## 130                                            NA                           NA
## 131                                            NA                           NA
## 132                                            NA                           NA
## 133                                            NA                           NA
## 134                                            NA                           NA
## 135                                            NA                           NA
## 136                                            NA                           NA
## 137                                             1                            1
## 138                                            NA                           NA
## 139                                            NA                           NA
## 140                                            NA                            1
## 141                                            NA                            0
## 142                                            NA                           NA
## 143                                            NA                           NA
## 144                                            NA                           NA
## 145                                            NA                           NA
## 146                                            NA                           NA
## 147                                            NA                           NA
## 148                                            NA                            0
## 149                                            NA                           NA
## 150                                            NA                           NA
## 151                                            NA                            1
## 152                                            NA                            1
## 153                                            NA                            0
## 154                                             1                            1
## 155                                            NA                           NA
## 156                                             0                           NA
## 157                                            NA                            0
## 158                                            NA                            0
## 159                                             0                           NA
## 160                                            NA                            0
## 161                                            NA                            0
## 162                                             1                            1
## 163                                            NA                            0
## 164                                            NA                           NA
## 165                                            NA                           NA
## 166                                            NA                           NA
## 167                                            NA                           NA
## 168                                            NA                           NA
## 169                                            NA                           NA
## 170                                            NA                           NA
## 171                                            NA                           NA
## 172                                            NA                           NA
## 173                                            NA                           NA
## 174                                            NA                           NA
## 175                                            NA                            0
## 176                                            NA                            0
## 177                                            NA                           NA
## 178                                             0                           NA
## 179                                             1                            1
## 180                                             0                           NA
## 181                                             0                           NA
## 182                                             1                           NA
## 183                                             0                           NA
## 184                                            NA                            0
## 185                                            NA                           NA
## 186                                            NA                           NA
## 187                                            NA                            0
## 188                                             0                           NA
## 189                                            NA                           NA
## 190                                            NA                           NA
## 191                                             0                           NA
## 192                                            NA                           NA
## 193                                            NA                           NA
## 194                                            NA                            0
## 195                                            NA                           NA
## 196                                            NA                           NA
## 197                                            NA                           NA
## 198                                            NA                           NA
## 199                                            NA                            0
## 200                                             0                            0
## 201                                            NA                            0
## 202                                            NA                           NA
## 203                                             0                           NA
## 204                                            NA                           NA
## 205                                            NA                           NA
## 206                                            NA                           NA
## 207                                            NA                           NA
## 208                                            NA                           NA
## 209                                            NA                           NA
## 210                                            NA                           NA
## 211                                            NA                            1
## 212                                            NA                           NA
## 213                                            NA                            0
## 214                                            NA                           NA
## 215                                            NA                           NA
## 216                                            NA                           NA
## 217                                            NA                           NA
## 218                                            NA                            0
## 219                                            NA                           NA
## 220                                            NA                            0
## 221                                            NA                           NA
## 222                                            NA                           NA
## 223                                            NA                           NA
## 224                                            NA                           NA
## 225                                             0                           NA
## 226                                            NA                           NA
## 227                                            NA                           NA
##     c155_global_FvsM used_joint_genotyping used _river_comparisons
## 1                  1                   Yes                    <NA>
## 2                 NA                   Yes                    <NA>
## 3                 NA                   Yes                    <NA>
## 4                  1                   Yes                    <NA>
## 5                  1                   Yes                    <NA>
## 6                  1                   Yes                    <NA>
## 7                  0                   Yes                    <NA>
## 8                 NA                   Yes                    <NA>
## 9                 NA                   Yes                    <NA>
## 10                NA                   Yes                    <NA>
## 11                 1                   Yes                     Yes
## 12                 0                   Yes                     Yes
## 13                NA                   Yes                     Yes
## 14                NA                   Yes                     Yes
## 15                NA                   Yes                     Yes
## 16                NA                   Yes                     Yes
## 17                NA                   Yes                     Yes
## 18                NA                   Yes                     Yes
## 19                NA                   Yes                     Yes
## 20                NA                   Yes                     Yes
## 21                 1                   Yes                    <NA>
## 22                NA                   Yes                    <NA>
## 23                NA                   Yes                    <NA>
## 24                 0                   Yes                    <NA>
## 25                 1                   Yes                     Yes
## 26                NA                   Yes                     Yes
## 27                NA                   Yes                     Yes
## 28                NA                   Yes                     Yes
## 29                NA                   Yes                     Yes
## 30                 0                   Yes                     Yes
## 31                NA                   Yes                     Yes
## 32                NA                   Yes                     Yes
## 33                NA                   Yes                     Yes
## 34                NA                   Yes                     Yes
## 35                NA                   Yes                    <NA>
## 36                 0                   Yes                    <NA>
## 37                NA                   Yes                    <NA>
## 38                NA                   Yes                    <NA>
## 39                 0                   Yes                    <NA>
## 40                 1                   Yes                    <NA>
## 41                 0                   Yes                    <NA>
## 42                 0                   Yes                    <NA>
## 43                NA                   Yes                    <NA>
## 44                NA                   Yes                    <NA>
## 45                NA                   Yes                    <NA>
## 46                NA                   Yes                    <NA>
## 47                NA                   Yes                    <NA>
## 48                NA                   Yes                    <NA>
## 49                NA                   Yes                    <NA>
## 50                 1                   Yes                    <NA>
## 51                NA                   Yes                    <NA>
## 52                NA                   Yes                    <NA>
## 53                 0                   Yes                    <NA>
## 54                NA                   Yes                    <NA>
## 55                NA                   Yes                    <NA>
## 56                NA                   Yes                    <NA>
## 57                NA                   Yes                    <NA>
## 58                 0                   Yes                    <NA>
## 59                 0                   Yes                    <NA>
## 60                NA                   Yes                    <NA>
## 61                NA                   Yes                    <NA>
## 62                 0                   Yes                    <NA>
## 63                 0                   Yes                    <NA>
## 64                 0                   Yes                    <NA>
## 65                 1                   Yes                    <NA>
## 66                 1                   Yes                    <NA>
## 67                NA                   Yes                    <NA>
## 68                NA                   Yes                    <NA>
## 69                 1                   Yes                    <NA>
## 70                 0                   Yes                    <NA>
## 71                NA                   Yes                    <NA>
## 72                NA                   Yes                    <NA>
## 73                NA                   Yes                    <NA>
## 74                 1                   Yes                    <NA>
## 75                 1                   Yes                    <NA>
## 76                 0                   Yes                    <NA>
## 77                 1                   Yes                    <NA>
## 78                 0                   Yes                    <NA>
## 79                 0                   Yes                    <NA>
## 80                NA                   Yes                    <NA>
## 81                 1                   Yes                     Yes
## 82                NA                   Yes                     Yes
## 83                NA                   Yes                     Yes
## 84                NA                   Yes                     Yes
## 85                NA                   Yes                     Yes
## 86                 0                   Yes                     Yes
## 87                NA                   Yes                     Yes
## 88                NA                   Yes                     Yes
## 89                NA                   Yes                     Yes
## 90                NA                   Yes                     Yes
## 91                 1                   Yes                    <NA>
## 92                NA                   Yes                    <NA>
## 93                 0                   Yes                    <NA>
## 94                NA                   Yes                    <NA>
## 95                 0                   Yes                    <NA>
## 96                 0                   Yes                    <NA>
## 97                NA                   Yes                    <NA>
## 98                NA                   Yes                    <NA>
## 99                NA                   Yes                    <NA>
## 100               NA                   Yes                    <NA>
## 101               NA                   Yes                    <NA>
## 102               NA                   Yes                    <NA>
## 103               NA                   Yes                    <NA>
## 104               NA                   Yes                    <NA>
## 105               NA                   Yes                    <NA>
## 106               NA                   Yes                    <NA>
## 107               NA                   Yes                    <NA>
## 108               NA                   Yes                    <NA>
## 109               NA                   Yes                    <NA>
## 110               NA                   Yes                    <NA>
## 111               NA                   Yes                    <NA>
## 112               NA                   Yes                    <NA>
## 113               NA                   Yes                    <NA>
## 114               NA                   Yes                    <NA>
## 115               NA                   Yes                    <NA>
## 116               NA                   Yes                    <NA>
## 117               NA                   Yes                    <NA>
## 118                0                   Yes                    <NA>
## 119                0                   Yes                    <NA>
## 120                1                   Yes                    <NA>
## 121                0                   Yes                    <NA>
## 122               NA                   Yes                    <NA>
## 123                1                   Yes                    <NA>
## 124                0                   Yes                    <NA>
## 125                0                   Yes                    <NA>
## 126               NA                   Yes                    <NA>
## 127               NA                   Yes                    <NA>
## 128               NA                   Yes                    <NA>
## 129               NA                   Yes                    <NA>
## 130               NA                   Yes                    <NA>
## 131               NA                   Yes                    <NA>
## 132               NA                   Yes                    <NA>
## 133               NA                   Yes                    <NA>
## 134               NA                   Yes                    <NA>
## 135               NA                   Yes                    <NA>
## 136               NA                   Yes                    <NA>
## 137                1                   Yes                    <NA>
## 138               NA                   Yes                     Yes
## 139               NA                   Yes                     Yes
## 140                1                   Yes                     Yes
## 141                0                   Yes                     Yes
## 142               NA                   Yes                     Yes
## 143               NA                   Yes                     Yes
## 144               NA                   Yes                     Yes
## 145               NA                   Yes                     Yes
## 146               NA                   Yes                     Yes
## 147               NA                   Yes                     Yes
## 148                0                   Yes                    <NA>
## 149               NA                   Yes                    <NA>
## 150               NA                   Yes                    <NA>
## 151                1                   Yes                    <NA>
## 152                1                   Yes                    <NA>
## 153                0                   Yes                    <NA>
## 154                1                   Yes                    <NA>
## 155               NA                   Yes                    <NA>
## 156                0                   Yes                    <NA>
## 157                0                   Yes                    <NA>
## 158                0                   Yes                    <NA>
## 159                0                   Yes                    <NA>
## 160                0                   Yes                    <NA>
## 161                0                   Yes                    <NA>
## 162                1                   Yes                    <NA>
## 163                0                   Yes                    <NA>
## 164               NA                   Yes                    <NA>
## 165               NA                   Yes                    <NA>
## 166               NA                   Yes                    <NA>
## 167               NA                   Yes                    <NA>
## 168               NA                   Yes                    <NA>
## 169               NA                   Yes                    <NA>
## 170               NA                   Yes                    <NA>
## 171               NA                   Yes                    <NA>
## 172               NA                   Yes                    <NA>
## 173               NA                   Yes                    <NA>
## 174               NA                   Yes                    <NA>
## 175                0                   Yes                    <NA>
## 176                0                   Yes                    <NA>
## 177               NA                   Yes                    <NA>
## 178                0                   Yes                    <NA>
## 179                1                   Yes                    <NA>
## 180                0                   Yes                    <NA>
## 181                0                   Yes                    <NA>
## 182                1                   Yes                    <NA>
## 183                0                   Yes                    <NA>
## 184                0                   Yes                    <NA>
## 185               NA                   Yes                    <NA>
## 186               NA                   Yes                    <NA>
## 187                0                   Yes                    <NA>
## 188                0                   Yes                    <NA>
## 189               NA                   Yes                    <NA>
## 190               NA                   Yes                    <NA>
## 191                0                   Yes                    <NA>
## 192               NA                   Yes                    <NA>
## 193               NA                   Yes                    <NA>
## 194                0                   Yes                    <NA>
## 195               NA                   Yes                    <NA>
## 196               NA                   Yes                    <NA>
## 197               NA                   Yes                    <NA>
## 198               NA                   Yes                    <NA>
## 199                0                   Yes                    <NA>
## 200                0                   Yes                    <NA>
## 201                0                   Yes                    <NA>
## 202               NA                   Yes                    <NA>
## 203                0                   Yes                    <NA>
## 204               NA                   Yes                    <NA>
## 205               NA                   Yes                    <NA>
## 206               NA                   Yes                    <NA>
## 207               NA                   Yes                     Yes
## 208               NA                   Yes                     Yes
## 209               NA                   Yes                     Yes
## 210               NA                   Yes                     Yes
## 211                1                   Yes                     Yes
## 212               NA                   Yes                    <NA>
## 213                0                   Yes                     Yes
## 214               NA                   Yes                     Yes
## 215               NA                   Yes                     Yes
## 216               NA                   Yes                     Yes
## 217               NA                   Yes                     Yes
## 218                0                   Yes                    <NA>
## 219               NA                   Yes                    <NA>
## 220                0                   Yes                    <NA>
## 221               NA                   Yes                    <NA>
## 222               NA                   Yes                    <NA>
## 223               NA                   Yes                    <NA>
## 224               NA                   Yes                    <NA>
## 225                0                   Yes                    <NA>
## 226               NA                   Yes                    <NA>
## 227               NA                   Yes                    <NA>
##     used_pilot_analysis wg_norm_depth    ecotype    sex samp_length O(HOM)
## 1                  <NA>     0.6849506     Marine female          15   3382
## 2                  <NA>     2.3553292 Freshwater female          14   3852
## 3                  <NA>     1.4800345 Freshwater female          14   3619
## 4                  <NA>     0.5374682     Marine female           4    730
## 5                  <NA>     0.7026082     Marine female          14   3304
## 6                  <NA>     0.5020058     Marine female           4   1278
## 7                  <NA>     1.6359764 Freshwater female           4   2192
## 8                  <NA>     0.8270414 Freshwater female          14   3373
## 9                  <NA>     1.0066092 Freshwater female           4   2153
## 10                 <NA>     1.0850730     Marine female           4   1654
## 11                 <NA>     0.4878640     Marine female          17   2830
## 12                 <NA>     0.8651173 Freshwater female          18   2984
## 13                 <NA>     1.3731481     Marine female          17   3307
## 14                 <NA>     0.8045064     Marine   male          17   2741
## 15                 <NA>     1.3648798     Marine female          17   2831
## 16                 <NA>     2.1426930     Marine female          17   3382
## 17                 <NA>     1.4323414 Freshwater female          18   3438
## 18                 <NA>     1.4249474 Freshwater female          18   3466
## 19                 <NA>     1.7432035 Freshwater female          18   3300
## 20                 <NA>     1.4343480 Freshwater female          18   3414
## 21                 <NA>     1.0560614     Marine female          11   3416
## 22                 <NA>     0.2388108 Freshwater   male          14   2189
## 23                 <NA>     1.2917555 Freshwater female          14   3688
## 24                 <NA>     3.3653854 Freshwater female          14   3822
## 25                 <NA>     0.7454121     Marine female          14   3304
## 26                 <NA>     1.1370784     Marine female          14   2929
## 27                 <NA>     1.0638894     Marine female          14   2845
## 28                 <NA>     0.6918268     Marine female          14   3139
## 29                 <NA>     0.7529911     Marine female          14   3252
## 30                 <NA>     1.5920580 Freshwater female          13   3806
## 31                 <NA>     1.5142402 Freshwater female          14   3788
## 32                 <NA>     1.5162031 Freshwater female          14   3816
## 33                 <NA>     1.5549021 Freshwater female          14   3711
## 34                 <NA>     1.1345803 Freshwater   male          14   2684
## 35                 <NA>     2.3256956 Freshwater female          14   3743
## 36                 <NA>     1.4180224 Freshwater female          14   3868
## 37                 <NA>     1.4086799 Freshwater female          14   3827
## 38                 <NA>     2.3403841 Freshwater female          14   3864
## 39                 <NA>     1.3365278 Freshwater female          14   3847
## 40                 <NA>     0.6451813     Marine female          15   3188
## 41                 <NA>     1.5962013 Freshwater female          11   3377
## 42                 <NA>     1.6120307 Freshwater female          14   3710
## 43                 <NA>     2.2106712 Freshwater female          14   3694
## 44                 <NA>     0.8067502 Freshwater female          17   3820
## 45                 <NA>     1.7448533 Freshwater female          14   3150
## 46                 <NA>     2.1585358 Freshwater female          14   3830
## 47                 <NA>     1.6178348 Freshwater female          14   3749
## 48                 <NA>     2.3118221 Freshwater female          11   3817
## 49                 <NA>     0.7622220 Freshwater female          14   3321
## 50                 <NA>     0.7169636     Marine female          14   3274
## 51                 <NA>     2.2276141 Freshwater female          14   3811
## 52                 <NA>     1.4107704 Freshwater female          14   3821
## 53                 <NA>     1.6770689 Freshwater female          14   3865
## 54                 <NA>     2.4247752 Freshwater female          14   3836
## 55                 <NA>     1.7239491 Freshwater female          14   3804
## 56                 <NA>     2.3930454 Freshwater female          14   3871
## 57                 <NA>     0.5948837 Freshwater female          14   3836
## 58                 <NA>     1.4550171 Freshwater female          13   3548
## 59                 <NA>     1.6439918 Freshwater female          16   3800
## 60                 <NA>     0.6504109 Freshwater female          15   3238
## 61                 <NA>     1.3984490 Freshwater female          15   3477
## 62                 <NA>     1.4375823 Freshwater female          11   3537
## 63                 <NA>     2.2386367 Freshwater female           3   3093
## 64                 <NA>     1.5359807 Freshwater female          12   3439
## 65                 <NA>     0.7497102     Marine female          14   3455
## 66                 <NA>     0.5168126     Marine female           4   1545
## 67                 <NA>     1.7884366 Freshwater female          14   3816
## 68                 <NA>     1.4725381 Freshwater female          11   3798
## 69                 <NA>     0.5199243     Marine female           4   1396
## 70                 <NA>     2.9629871 Freshwater female          11   3763
## 71                 <NA>     0.7757477 Freshwater female          14   3321
## 72                 <NA>     1.3699633 Freshwater female           4   3075
## 73                 <NA>     2.2706840 Freshwater female          14   3851
## 74                 <NA>     0.4848061     Marine female           4   1614
## 75                 <NA>     0.7417463     Marine female          14   3268
## 76                 <NA>     2.4103507 Freshwater female          14   3880
## 77                 <NA>     0.7306434     Marine female          14   3329
## 78                 <NA>     0.7965982 Freshwater female          14   3374
## 79                 <NA>     0.8038521 Freshwater female          14   3419
## 80                 <NA>     1.6028817 Freshwater   male          15   3103
## 81                 <NA>     0.5343506     Marine female          18   2843
## 82                 <NA>     0.4699554     Marine female          18   2989
## 83                 <NA>     0.3299840     Marine female          17   2314
## 84                 <NA>     0.4799899     Marine female          17   2748
## 85                 <NA>     0.6461944     Marine female          18   3164
## 86                 <NA>     1.2179789 Freshwater female          19   3667
## 87                 <NA>     0.9831386 Freshwater female          19   3670
## 88                 <NA>     1.0767117 Freshwater female          19   3454
## 89                 <NA>     1.3577359 Freshwater female          19   3791
## 90                 <NA>     1.0543748 Freshwater female          19   3421
## 91                 <NA>     0.8396474     Marine female          14   3429
## 92                 <NA>     2.4631694 Freshwater female          11   3820
## 93                 <NA>     1.4118588 Freshwater female          11   3765
## 94                 <NA>     0.7804802 Freshwater female          14   3503
## 95                 <NA>     3.0811556 Freshwater female          14   3735
## 96                 <NA>     1.0810420 Freshwater female          14   3669
## 97                  Yes     1.6117281 Freshwater female          14   2833
## 98                  Yes     1.5025336 Freshwater female          14   2987
## 99                  Yes     2.4864625 Freshwater female          14   3909
## 100                 Yes     1.5502741 Freshwater female          14   2938
## 101                 Yes     0.7193451 Freshwater female          14   3453
## 102                 Yes     1.5097536 Freshwater female          14   2950
## 103                 Yes     2.3767589 Freshwater female          14   3865
## 104                 Yes     2.2882877 Freshwater female          14   3835
## 105                 Yes     1.5083706 Freshwater female          14   2960
## 106                 Yes     0.7557168 Freshwater female          14   3352
## 107                 Yes     1.4453855 Freshwater female          14   2953
## 108                 Yes     1.5498538 Freshwater female          14   2940
## 109                 Yes     1.6572115 Freshwater female          14   3032
## 110                 Yes     1.5847858 Freshwater female          14   2952
## 111                 Yes     2.2934529 Freshwater female          14   3826
## 112                 Yes     1.4353749 Freshwater female          14   3060
## 113                 Yes     1.5178244 Freshwater female          14   2920
## 114                 Yes     0.7958166 Freshwater female          14   3463
## 115                 Yes     2.4039353 Freshwater female          14   3855
## 116                 Yes     2.4703915 Freshwater female          14   3810
## 117                <NA>     2.1904474 Freshwater female          14   3878
## 118                <NA>     1.9278299 Freshwater female          14   3834
## 119                <NA>     1.1286510 Freshwater female          14   3336
## 120                <NA>     0.7669173     Marine female          14   3384
## 121                <NA>     0.8153668 Freshwater female          14   3375
## 122                <NA>     1.3803423 Freshwater female          16   3835
## 123                <NA>     0.7993700     Marine female          11   3438
## 124                <NA>     0.5472449 Freshwater female           4   2083
## 125                <NA>     1.3804163 Freshwater female          14   3829
## 126                <NA>     2.4248297 Freshwater female          14   3724
## 127                <NA>     2.4315721 Freshwater female          14   3846
## 128                <NA>     2.0464793 Freshwater female          14   3867
## 129                <NA>     2.3466848 Freshwater female          14   3845
## 130                <NA>     2.3908255 Freshwater female          14   3807
## 131                <NA>     2.5373425 Freshwater female          14   3877
## 132                <NA>     2.8931416 Freshwater female          14   3822
## 133                <NA>     2.4703497 Freshwater female          14   3828
## 134                <NA>     1.6373087 Freshwater female          14   3858
## 135                <NA>     2.0861268 Freshwater female          14   3894
## 136                <NA>     2.0477834 Freshwater female          14   3867
## 137                <NA>     0.5498641     Marine female          14   3268
## 138                <NA>     1.1991732     Marine female          17   3397
## 139                <NA>     1.1202526     Marine female          17   3272
## 140                <NA>     1.0399630     Marine female          17   3371
## 141                <NA>     2.1189994 Freshwater female          17   3761
## 142                <NA>     2.8106664 Freshwater female          17   3754
## 143                <NA>     1.9798941 Freshwater   male          17   3017
## 144                <NA>     2.2538158 Freshwater   male          17   3005
## 145                <NA>     2.4949858 Freshwater female          17   3818
## 146                <NA>     1.1200892     Marine female          17   3422
## 147                <NA>     0.7969474     Marine female          17   3311
## 148                <NA>     1.5546823 Freshwater female          11   3838
## 149                <NA>     2.2903742 Freshwater female          14   3839
## 150                <NA>     1.9395086 Freshwater female           4   2478
## 151                <NA>     0.5037678     Marine female           3    197
## 152                <NA>     0.7710100     Marine female          14   3419
## 153                <NA>     2.2538990 Freshwater female           4    912
## 154                <NA>     0.8424049     Marine   male          11   2143
## 155                <NA>     0.6851245 Freshwater female          14   3297
## 156                <NA>     0.3658525 Freshwater female          14   2349
## 157                <NA>     2.0102874 Freshwater female          14   3740
## 158                <NA>     1.8538903 Freshwater female           4   2716
## 159                <NA>     1.5355805 Freshwater female          11   3410
## 160                <NA>     0.7264593 Freshwater female          17   3303
## 161                <NA>     0.8395585 Freshwater female          14   3242
## 162                <NA>     0.5258849     Marine female           4   2078
## 163                <NA>     2.2118217 Freshwater female          14   3732
## 164                <NA>     1.4440474 Freshwater female          14   3830
## 165                <NA>     2.0801201 Freshwater female          17   3874
## 166                <NA>     1.7273823 Freshwater female          17   3682
## 167                <NA>     2.0801138 Freshwater female          17   3765
## 168                <NA>     2.0695983 Freshwater female          17   3778
## 169                <NA>     1.8873688 Freshwater female          17   3783
## 170                <NA>     2.0130179 Freshwater female          17   3793
## 171                <NA>     1.7134147 Freshwater female          17   3739
## 172                <NA>     2.0014454 Freshwater female          17   3471
## 173                <NA>     1.7836642 Freshwater female          17   3817
## 174                <NA>     1.3158736 Freshwater female          17   3843
## 175                <NA>     1.4627901 Freshwater   male          14   2867
## 176                <NA>     1.5287475 Freshwater female          14   3704
## 177                <NA>     2.2190249 Freshwater female          15   3875
## 178                <NA>     1.7042274 Freshwater female          16   3465
## 179                <NA>     0.4274776     Marine female           4   1098
## 180                <NA>     1.8284334 Freshwater female          11   3364
## 181                <NA>     1.5050920 Freshwater female          11   3463
## 182                <NA>     1.4493094     Marine female          15   3360
## 183                <NA>     1.4687684 Freshwater female          16   3519
## 184                <NA>     1.6909613 Freshwater female           3   2000
## 185                <NA>     0.6946182 Freshwater female          14   3836
## 186                <NA>     1.9538070 Freshwater female           4   2595
## 187                <NA>     1.4150368 Freshwater female          14   3322
## 188                <NA>     1.3995207 Freshwater female          16   3377
## 189                <NA>     2.0975582 Freshwater female          14   3812
## 190                <NA>     2.2469878 Freshwater female          11   3841
## 191                <NA>     1.4931082 Freshwater female          16   3399
## 192                <NA>     2.4351882 Freshwater female          14   3901
## 193                <NA>     1.5232511 Freshwater female          17   3740
## 194                <NA>     1.3564929 Freshwater female          14   2844
## 195                <NA>     0.6574794 Freshwater female          14   3405
## 196                <NA>     1.6187013 Freshwater female          14   3802
## 197                <NA>     2.0666936 Freshwater female          14   3818
## 198                <NA>     2.3104468 Freshwater female          14   3827
## 199                <NA>     1.9013754 Freshwater female          15   3764
## 200                <NA>     1.4531613 Freshwater female          14   3335
## 201                <NA>     2.1253919 Freshwater female          14   3878
## 202                <NA>     2.3799560 Freshwater female          14   3843
## 203                <NA>     1.5878779 Freshwater female          11   3390
## 204                <NA>     2.2704204 Freshwater female          14   3857
## 205                <NA>     0.7655431 Freshwater female          14   3489
## 206                <NA>     1.0359457     Marine female           6   1617
## 207                <NA>     0.6902854     Marine female          14   3302
## 208                <NA>     0.6985398     Marine female          14   3323
## 209                <NA>     0.7077671     Marine female          14   3246
## 210                <NA>     1.3967808     Marine female          14   2939
## 211                <NA>     0.6833612     Marine female          14   3300
## 212                <NA>     1.2769341 Freshwater female           6   2845
## 213                <NA>     1.4403373 Freshwater female          15   3676
## 214                <NA>     1.4511802 Freshwater female          15   3761
## 215                <NA>     1.4965529 Freshwater female          15   3688
## 216                <NA>     1.4960439 Freshwater female          15   3619
## 217                <NA>     1.4551439 Freshwater female          15   3677
## 218                <NA>     2.2754477 Freshwater female          11   3812
## 219                <NA>     2.3915016 Freshwater female          11   3752
## 220                <NA>     2.3704515 Freshwater female          11   3805
## 221                <NA>     1.9100514 Freshwater female          14   3827
## 222                <NA>     1.7311785 Freshwater female          14   3800
## 223                <NA>     1.3781070 Freshwater female          14   3403
## 224                <NA>     1.8285512 Freshwater female          14   3591
## 225                <NA>     0.4127094 Freshwater female          16   2122
## 226                <NA>     2.1754838 Freshwater female          14   3778
## 227                <NA>     2.9936058 Freshwater female          14   3811
##     E(HOM) N_SITES        F  prop_hom    prop_het het_status
## 1   2871.6    3510  0.79950 0.9635328 0.036467236 likely-hom
## 2   3150.2    3856  0.99433 0.9989627 0.001037344 likely-hom
## 3   3043.1    3725  0.84454 0.9715436 0.028456376 likely-hom
## 4    658.9     732  0.97265 0.9972678 0.002732240 likely-hom
## 5   2800.8    3421  0.81134 0.9657995 0.034200526 likely-hom
## 6   1142.2    1283  0.96450 0.9961029 0.003897116 likely-hom
## 7   1779.7    2192  1.00000 1.0000000 0.000000000 likely-hom
## 8   2811.3    3439  0.89485 0.9808084 0.019191625 likely-hom
## 9   1828.9    2188  0.90253 0.9840037 0.015996344 likely-hom
## 10  1402.8    1670  0.94011 0.9904192 0.009580838 likely-hom
## 11  2393.5    2911  0.84347 0.9721745 0.027825490 likely-hom
## 12  2493.0    3040  0.89762 0.9815789 0.018421053 likely-hom
## 13  2870.1    3509  0.68381 0.9424337 0.057566258 likely-hom
## 14  2796.2    3400 -0.09135 0.8061765 0.193823529 likely-het
## 15  2892.7    3524 -0.09765 0.8033485 0.196651532 likely-het
## 16  2882.7    3518  0.78594 0.9613417 0.038658329 likely-hom
## 17  2857.3    3497  0.90777 0.9831284 0.016871604 likely-hom
## 18  2919.5    3575  0.83372 0.9695105 0.030489510 likely-hom
## 19  2906.7    3561  0.60110 0.9267060 0.073294019 likely-hom
## 20  2832.0    3466  0.91798 0.9849971 0.015002885 likely-hom
## 21  2916.3    3576  0.75748 0.9552573 0.044742729 likely-hom
## 22  1945.2    2368  0.57658 0.9244088 0.075591216 likely-hom
## 23  3030.8    3705  0.97478 0.9954116 0.004588394 likely-hom
## 24  3132.9    3835  0.98148 0.9966102 0.003389831 likely-hom
## 25  2803.8    3425  0.80521 0.9646715 0.035328467 likely-hom
## 26  3092.9    3770 -0.24210 0.7769231 0.223076923 likely-het
## 27  2807.9    3419  0.06066 0.8321147 0.167885347 likely-het
## 28  2675.6    3255  0.79978 0.9643625 0.035637481 likely-hom
## 29  2737.1    3341  0.85263 0.9733613 0.026638731 likely-hom
## 30  3129.6    3831  0.96435 0.9934743 0.006525711 likely-hom
## 31  3130.2    3830  0.93998 0.9890339 0.010966057 likely-hom
## 32  3145.8    3846  0.95715 0.9921997 0.007800312 likely-hom
## 33  3065.9    3747  0.94715 0.9903923 0.009607686 likely-hom
## 34  2690.2    3275 -0.01055 0.8195420 0.180458015 likely-het
## 35  3119.2    3819  0.89140 0.9800995 0.019900498 likely-hom
## 36  3169.7    3878  0.98588 0.9974214 0.002578649 likely-hom
## 37  3140.0    3841  0.98003 0.9963551 0.003644884 likely-hom
## 38  3162.7    3873  0.98733 0.9976762 0.002323780 likely-hom
## 39  3153.6    3862  0.97882 0.9961160 0.003883998 likely-hom
## 40  2720.2    3322  0.77734 0.9596629 0.040337146 likely-hom
## 41  2953.4    3609  0.64613 0.9357163 0.064283735 likely-hom
## 42  3038.3    3714  0.99408 0.9989230 0.001077006 likely-hom
## 43  3080.2    3767  0.89371 0.9806212 0.019378816 likely-hom
## 44  3139.3    3842  0.96869 0.9942738 0.005726184 likely-hom
## 45  3020.5    3694  0.19233 0.8527342 0.147265836 likely-het
## 46  3160.4    3865  0.95033 0.9909444 0.009055627 likely-hom
## 47  3082.3    3767  0.97371 0.9952217 0.004778338 likely-hom
## 48  3127.5    3828  0.98430 0.9971264 0.002873563 likely-hom
## 49  2833.8    3463  0.77432 0.9589951 0.041004909 likely-hom
## 50  2823.6    3450  0.71903 0.9489855 0.051014493 likely-hom
## 51  3138.4    3841  0.95730 0.9921895 0.007810466 likely-hom
## 52  3135.5    3841  0.97165 0.9947930 0.005206977 likely-hom
## 53  3183.1    3895  0.95786 0.9922978 0.007702182 likely-hom
## 54  3177.7    3890  0.92419 0.9861183 0.013881748 likely-hom
## 55  3185.8    3898  0.86801 0.9758851 0.024114931 likely-hom
## 56  3178.1    3891  0.97195 0.9948599 0.005140067 likely-hom
## 57  3155.0    3862  0.96322 0.9932677 0.006732263 likely-hom
## 58  2954.2    3611  0.90408 0.9825533 0.017446691 likely-hom
## 59  3127.3    3825  0.96417 0.9934641 0.006535948 likely-hom
## 60  2742.8    3354  0.81022 0.9654144 0.034585569 likely-hom
## 61  2892.1    3537  0.90696 0.9830365 0.016963528 likely-hom
## 62  2950.9    3608  0.89194 0.9803215 0.019678492 likely-hom
## 63  2529.3    3103  0.98257 0.9967773 0.003222688 likely-hom
## 64  2921.1    3570  0.79812 0.9633053 0.036694678 likely-hom
## 65  2851.3    3487  0.94966 0.9908231 0.009176943 likely-hom
## 66  1373.2    1555  0.94499 0.9935691 0.006430868 likely-hom
## 67  3188.2    3903  0.87829 0.9777095 0.022290546 likely-hom
## 68  3144.1    3846  0.93161 0.9875195 0.012480499 likely-hom
## 69  1244.6    1400  0.97425 0.9971429 0.002857143 likely-hom
## 70  3116.4    3813  0.92822 0.9868870 0.013113034 likely-hom
## 71  2782.3    3394  0.88067 0.9784915 0.021508544 likely-hom
## 72  2524.7    3083  0.98567 0.9974051 0.002594875 likely-hom
## 73  3159.6    3869  0.97463 0.9953476 0.004652365 likely-hom
## 74  1426.7    1619  0.97400 0.9969117 0.003088326 likely-hom
## 75  2800.4    3418  0.75712 0.9561147 0.043885313 likely-hom
## 76  3173.0    3885  0.99298 0.9987130 0.001287001 likely-hom
## 77  2841.9    3472  0.77306 0.9588134 0.041186636 likely-hom
## 78  2804.1    3428  0.91344 0.9842474 0.015752625 likely-hom
## 79  2850.6    3484  0.89738 0.9813433 0.018656716 likely-hom
## 80  3116.4    3806 -0.01947 0.8152916 0.184708355 likely-het
## 81  2490.5    3007  0.68246 0.9454606 0.054539408 likely-hom
## 82  2542.0    3092  0.81274 0.9666882 0.033311772 likely-hom
## 83  1989.0    2373  0.84635 0.9751370 0.024863043 likely-hom
## 84  2344.4    2853  0.79355 0.9631966 0.036803365 likely-hom
## 85  2683.7    3275  0.81229 0.9661069 0.033893130 likely-hom
## 86  3010.0    3687  0.97046 0.9945755 0.005424464 likely-hom
## 87  3031.0    3709  0.94248 0.9894850 0.010514964 likely-hom
## 88  2832.7    3471  0.97336 0.9951023 0.004897724 likely-hom
## 89  3118.2    3821  0.95731 0.9921487 0.007851348 likely-hom
## 90  2821.9    3444  0.96303 0.9933217 0.006678281 likely-hom
## 91  2887.2    3534  0.83765 0.9702886 0.029711375 likely-hom
## 92  3155.3    3862  0.94057 0.9891248 0.010875194 likely-hom
## 93  3087.5    3779  0.97975 0.9962953 0.003704684 likely-hom
## 94  2934.7    3600  0.85420 0.9730556 0.026944444 likely-hom
## 95  3072.3    3758  0.96646 0.9938797 0.006120277 likely-hom
## 96  3036.1    3715  0.93224 0.9876178 0.012382234 likely-hom
## 97  3048.8    3714 -0.32440 0.7627894 0.237210555 likely-het
## 98  3091.4    3768 -0.15428 0.7927282 0.207271762 likely-het
## 99  3208.1    3927  0.97496 0.9954163 0.004583652 likely-hom
## 100 3128.0    3819 -0.27490 0.7693113 0.230688662 likely-het
## 101 2892.5    3538  0.86833 0.9759751 0.024024873 likely-hom
## 102 3107.2    3793 -0.22921 0.7777485 0.222251516 likely-het
## 103 3208.3    3926  0.91501 0.9844626 0.015537443 likely-hom
## 104 3181.7    3893  0.91846 0.9851015 0.014898536 likely-hom
## 105 3034.7    3694 -0.11328 0.8012994 0.198700596 likely-het
## 106 2861.8    3498  0.77051 0.9582619 0.041738136 likely-hom
## 107 3049.8    3711 -0.14646 0.7957424 0.204257613 likely-het
## 108 3064.8    3743 -0.18401 0.7854662 0.214533796 likely-het
## 109 3083.6    3760 -0.07622 0.8063830 0.193617021 likely-het
## 110 3064.7    3726 -0.17045 0.7922705 0.207729469 likely-het
## 111 3139.9    3841  0.97861 0.9960948 0.003905233 likely-hom
## 112 3077.4    3750 -0.02594 0.8160000 0.184000000 likely-het
## 113 3103.1    3790 -0.26660 0.7704485 0.229551451 likely-het
## 114 2971.2    3641  0.73425 0.9511123 0.048887668 likely-hom
## 115 3183.4    3896  0.94246 0.9894764 0.010523614 likely-hom
## 116 3158.2    3862  0.92612 0.9865355 0.013464526 likely-hom
## 117 3195.7    3911  0.95387 0.9915623 0.008437740 likely-hom
## 118 3153.4    3860  0.96320 0.9932642 0.006735751 likely-hom
## 119 2957.8    3620  0.57111 0.9215470 0.078453039 likely-hom
## 120 2803.3    3428  0.92956 0.9871645 0.012835473 likely-hom
## 121 2822.0    3455  0.87362 0.9768452 0.023154848 likely-hom
## 122 3148.5    3852  0.97583 0.9955867 0.004413292 likely-hom
## 123 2921.5    3570  0.79644 0.9630252 0.036974790 likely-hom
## 124 1735.0    2086  0.99145 0.9985618 0.001438159 likely-hom
## 125 3175.5    3888  0.91720 0.9848251 0.015174897 likely-hom
## 126 3091.7    3781  0.91731 0.9849246 0.015075377 likely-hom
## 127 3172.1    3884  0.94662 0.9902163 0.009783728 likely-hom
## 128 3179.9    3888  0.97034 0.9945988 0.005401235 likely-hom
## 129 3158.8    3867  0.96893 0.9943108 0.005689165 likely-hom
## 130 3124.7    3827  0.97152 0.9947740 0.005226026 likely-hom
## 131 3192.4    3909  0.95534 0.9918138 0.008186237 likely-hom
## 132 3182.2    3895  0.89758 0.9812580 0.018741977 likely-hom
## 133 3186.5    3897  0.90289 0.9822941 0.017705928 likely-hom
## 134 3170.6    3884  0.96356 0.9933059 0.006694130 likely-hom
## 135 3202.6    3918  0.96645 0.9938744 0.006125574 likely-hom
## 136 3192.9    3908  0.94266 0.9895087 0.010491300 likely-hom
## 137 2783.3    3407  0.77713 0.9592016 0.040798356 likely-hom
## 138 2892.0    3539  0.78052 0.9598757 0.040124329 likely-hom
## 139 2785.9    3399  0.79286 0.9626361 0.037363931 likely-hom
## 140 2863.8    3504  0.79226 0.9620434 0.037956621 likely-hom
## 141 3138.5    3843  0.88361 0.9786625 0.021337497 likely-hom
## 142 3100.3    3796  0.93963 0.9889357 0.011064278 likely-hom
## 143 2954.2    3615  0.09499 0.8345781 0.165421853 likely-het
## 144 2990.2    3652  0.02239 0.8228368 0.177163198 likely-het
## 145 3135.8    3840  0.96876 0.9942708 0.005729167 likely-hom
## 146 2893.7    3543  0.81365 0.9658482 0.034151849 likely-hom
## 147 2826.1    3452  0.77471 0.9591541 0.040845886 likely-hom
## 148 3150.2    3854  0.97727 0.9958485 0.004151531 likely-hom
## 149 3154.7    3856  0.97576 0.9955913 0.004408714 likely-hom
## 150 2029.0    2478  1.00000 1.0000000 0.000000000 likely-hom
## 151  175.3     197  1.00000 1.0000000 0.000000000 likely-hom
## 152 2867.9    3516  0.85032 0.9724118 0.027588168 likely-hom
## 153  751.3     912  1.00000 1.0000000 0.000000000 likely-hom
## 154 2056.6    2481  0.20354 0.8637646 0.136235389 likely-het
## 155 2797.5    3426  0.79475 0.9623468 0.037653240 likely-hom
## 156 1969.8    2372  0.94282 0.9903035 0.009696459 likely-hom
## 157 3088.0    3781  0.94083 0.9891563 0.010843692 likely-hom
## 158 2224.3    2722  0.98795 0.9977957 0.002204262 likely-hom
## 159 2877.2    3519  0.83017 0.9690253 0.030974709 likely-hom
## 160 2762.4    3371  0.88827 0.9798279 0.020172056 likely-hom
## 161 2683.3    3272  0.94904 0.9908313 0.009168704 likely-hom
## 162 1790.6    2092  0.95355 0.9933078 0.006692161 likely-hom
## 163 3066.5    3750  0.97366 0.9952000 0.004800000 likely-hom
## 164 3153.9    3856  0.96297 0.9932573 0.006742739 likely-hom
## 165 3181.1    3895  0.97058 0.9946085 0.005391528 likely-hom
## 166 3035.3    3714  0.95285 0.9913840 0.008616047 likely-hom
## 167 3099.9    3793  0.95960 0.9926180 0.007382020 likely-hom
## 168 3119.5    3815  0.94680 0.9903014 0.009698558 likely-hom
## 169 3129.5    3827  0.93692 0.9885027 0.011497256 likely-hom
## 170 3138.7    3840  0.93298 0.9877604 0.012239583 likely-hom
## 171 3070.6    3759  0.97095 0.9946794 0.005320564 likely-hom
## 172 2850.4    3480  0.98571 0.9974138 0.002586207 likely-hom
## 173 3147.5    3852  0.95032 0.9909138 0.009086189 likely-hom
## 174 3151.9    3860  0.97599 0.9955959 0.004404145 likely-hom
## 175 2767.0    3358  0.16922 0.8537820 0.146217987 likely-het
## 176 3057.6    3741  0.94586 0.9901096 0.009890404 likely-hom
## 177 3180.8    3896  0.97064 0.9946099 0.005390144 likely-hom
## 178 2896.1    3541  0.88215 0.9785371 0.021462864 likely-hom
## 179  987.6    1100  0.98221 0.9981818 0.001818182 likely-hom
## 180 2992.8    3656  0.55968 0.9201313 0.079868709 likely-hom
## 181 2879.6    3519  0.91242 0.9840864 0.015913612 likely-hom
## 182 2905.6    3556  0.69863 0.9448819 0.055118110 likely-hom
## 183 2928.5    3589  0.89401 0.9804960 0.019504040 likely-hom
## 184 1629.9    2000  1.00000 1.0000000 0.000000000 likely-hom
## 185 3160.1    3867  0.95615 0.9919834 0.008016550 likely-hom
## 186 2117.8    2596  0.99791 0.9996148 0.000385208 likely-hom
## 187 2736.5    3344  0.96379 0.9934211 0.006578947 likely-hom
## 188 2916.7    3570  0.70457 0.9459384 0.054061625 likely-hom
## 189 3140.6    3844  0.95451 0.9916753 0.008324662 likely-hom
## 190 3195.0    3912  0.90097 0.9818507 0.018149284 likely-hom
## 191 2849.0    3479  0.87301 0.9770049 0.022995114 likely-hom
## 192 3197.7    3913  0.98322 0.9969333 0.003066701 likely-hom
## 193 3135.6    3838  0.86048 0.9744659 0.025534132 likely-hom
## 194 3102.1    3788 -0.37631 0.7507920 0.249208025 likely-het
## 195 2837.3    3475  0.89024 0.9798561 0.020143885 likely-hom
## 196 3136.2    3839  0.94736 0.9903621 0.009637927 likely-hom
## 197 3154.4    3860  0.94048 0.9891192 0.010880829 likely-hom
## 198 3156.6    3864  0.94770 0.9904244 0.009575569 likely-hom
## 199 3136.6    3834  0.89962 0.9817423 0.018257694 likely-hom
## 200 2885.8    3531  0.69622 0.9444916 0.055508355 likely-hom
## 201 3176.7    3888  0.98594 0.9974280 0.002572016 likely-hom
## 202 3170.6    3876  0.95322 0.9914861 0.008513932 likely-hom
## 203 2885.6    3524  0.79010 0.9619750 0.038024972 likely-hom
## 204 3163.2    3869  0.98300 0.9968984 0.003101577 likely-hom
## 205 2917.6    3579  0.86392 0.9748533 0.025146689 likely-hom
## 206 1374.9    1624  0.97190 0.9956897 0.004310345 likely-hom
## 207 2814.1    3446  0.77212 0.9582124 0.041787580 likely-hom
## 208 2804.3    3435  0.82243 0.9673945 0.032605531 likely-hom
## 209 2777.1    3401  0.75158 0.9544252 0.045574831 likely-hom
## 210 2863.1    3473  0.12443 0.8462424 0.153757558 likely-het
## 211 2819.7    3451  0.76080 0.9562446 0.043755433 likely-hom
## 212 2334.2    2848  0.99416 0.9989466 0.001053371 likely-hom
## 213 3039.1    3719  0.93676 0.9884378 0.011562248 likely-hom
## 214 3085.8    3775  0.97969 0.9962914 0.003708609 likely-hom
## 215 3100.7    3799  0.84105 0.9707818 0.029218215 likely-hom
## 216 3050.8    3732  0.83412 0.9697213 0.030278671 likely-hom
## 217 3031.4    3708  0.95418 0.9916397 0.008360302 likely-hom
## 218 3128.4    3827  0.97853 0.9960805 0.003919519 likely-hom
## 219 3077.0    3766  0.97968 0.9962825 0.003717472 likely-hom
## 220 3129.1    3829  0.96571 0.9937320 0.006267955 likely-hom
## 221 3159.5    3865  0.94614 0.9901682 0.009831824 likely-hom
## 222 3137.9    3837  0.94707 0.9903570 0.009642950 likely-hom
## 223 2788.5    3417  0.97772 0.9959028 0.004097161 likely-hom
## 224 2961.1    3619  0.95744 0.9922631 0.007736944 likely-hom
## 225 1764.2    2131  0.97547 0.9957766 0.004223369 likely-hom
## 226 3100.4    3794  0.97693 0.9957828 0.004217185 likely-hom
## 227 3154.7    3859  0.93185 0.9875615 0.012438456 likely-hom
read_tsv(het_file)
## Rows: 227 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (1): INDV
## dbl (4): O(HOM), E(HOM), N_SITES, F
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## # A tibble: 227 × 5
##    INDV            `O(HOM)` `E(HOM)` N_SITES     F
##    <chr>              <dbl>    <dbl>   <dbl> <dbl>
##  1 AKMA|X|2001#102     3382    2872.    3510 0.800
##  2 AKST|X|2001#03      3852    3150.    3856 0.994
##  3 ANSR_X_2009#01      3619    3043.    3725 0.845
##  4 ANTL                 730     659.     732 0.973
##  5 BARW|X|2012#04      3304    2801.    3421 0.811
##  6 BDGB                1278    1142.    1283 0.964
##  7 BEPA                2192    1780.    2192 1    
##  8 BHAR|X|2011#02      3373    2811.    3439 0.895
##  9 BIGL                2153    1829.    2188 0.903
## 10 BIGR                1654    1403.    1670 0.940
## # ℹ 217 more rows
# Get subset of sample names that excludes Jones et al. 2012 samples and males

vcf_samples_filt <- filter(tab_annot, sex=="female", samp_length > 6, desc=="MYH3C3", type=="real")$sample.id
# make filtered version of PCA with males and Jones et al. 2012 samples
# Open GDS file
genofile <- snpgdsOpen("all.gds")

# Run PCA
pca_filter <- snpgdsPCA(genofile, num.thread=2, autosome.only = FALSE, sample.id = vcf_samples_filt)
## Principal Component Analysis (PCA) on genotypes:
## Excluding 394 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
##     # of samples: 198
##     # of SNPs: 3,176
##     using 2 threads
##     # of principal components: 32
## PCA:    the sum of all selected genotypes (0,1,2) = 985378
## CPU capabilities: Double-Precision SSE2
## Sun Jul 13 22:16:22 2025    (internal increment: 4920)
## [..................................................]  0%, ETC: ---        [==================================================] 100%, completed, 1s
## Sun Jul 13 22:16:23 2025    Begin (eigenvalues and eigenvectors)
## Sun Jul 13 22:16:23 2025    Done.
snpgdsClose(genofile)

# variance proportion (%)
pc.percent_filter <- round(pca_filter$varprop*100, 2)
PC1_lab_filter <- paste("PC1 (", pc.percent_filter[1], "%)", sep = "")
PC2_lab_filter <- paste("PC2 (", pc.percent_filter[2], "%)", sep = "")

# make a new data.frame
tab_filter <- data.frame(sample.id = pca_filter$sample.id,
    EV1_filter = pca_filter$eigenvect[,1],    # the first eigenvector
    EV2_filter = pca_filter$eigenvect[,2],    # the second eigenvector
    EV3_filter = pca_filter$eigenvect[,3],    # the third eigenvector
    EV4_filter = pca_filter$eigenvect[,4],    # the fourth eigenvector
    stringsAsFactors = FALSE)

# Add to table
tab_annot <- left_join(tab_annot, tab_filter)
## Joining with `by = join_by(sample.id)`
# Make plot of all PCA without filtering where shape is het status
xlab
## function (label) 
## {
##     labs(x = label)
## }
## <bytecode: 0x2ac85a48a2a0>
## <environment: namespace:ggplot2>
tab_annot %>%
  ggplot(aes(EV1, EV2, color = wg_norm_depth)) +
  geom_point(aes(shape = het_status), size = 3,) +
  scale_color_viridis_c(option = "magma") +
  theme_cowplot(8) +
  panel_border(color="black", size=0.75) +
  xlab(PC1_lab) +
  ylab(PC2_lab)

# Make plot of all PCA without filtering where shape is het status with labels
tab_annot %>%
  ggplot(aes(EV1, EV2, color = wg_norm_depth)) +
  geom_point(aes(shape = het_status), size = 3,) +
  geom_label_repel(aes(label = acronym),
                   size = 3,
                  box.padding   = 0.5,
                  point.padding = 0.5,
                  max.overlaps = 50, 
                  nudge_x = 0.001,
                  segment.color = 'grey50') +
  scale_color_viridis_c(option = "magma") +
  theme_cowplot(20) +
  panel_border(color="black", size=0.75) +
  xlab(PC1_lab) +
  ylab(PC2_lab)
## Warning: ggrepel: 108 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Make plot of all PCA without filtering where shape is marine or freshwater
tab_annot %>%
  ggplot(aes(EV1, EV2, color = wg_norm_depth)) +
  geom_point(aes(shape = ecotype), size = 3,) +
  scale_color_viridis_c(option = "magma") +
  theme_cowplot(8) +
  panel_border(color="black", size=0.75) +
  xlab(PC1_lab) +
  ylab(PC2_lab)

# Make plot of all PCA without filtering where shape is marine or freshwater with labels
tab_annot %>%
  ggplot(aes(EV1, EV2, color = wg_norm_depth)) +
  geom_point(aes(shape = ecotype), size = 3,) +
  scale_color_viridis_c(option = "magma") +
    theme_cowplot(20) +
  panel_border(color="black", size=0.75) +
  geom_label_repel(aes(label = acronym),
                   size = 3,
                  box.padding   = 0.5,
                  point.padding = 0.5,
                  max.overlaps = 50, 
                  nudge_x = 0.001,
                  segment.color = 'grey50') +
  xlab(PC1_lab) +
  ylab(PC2_lab)
## Warning: ggrepel: 108 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

Remake plots with filtering out males and Jones et al. 2012 samples before running the PCA

# Make plot of filtered PCA where shape is het status
tab_annot %>%
  ggplot(aes(EV1_filter, EV2_filter, color = wg_norm_depth)) +
  geom_point(aes(shape = het_status), size = 3,) +
  scale_color_viridis_c(option = "magma") +
  theme_cowplot(8) +
  panel_border(color="black", size=0.75) +
  xlab(PC1_lab_filter) +
  ylab(PC2_lab_filter)
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_point()`).

# Make plot of filtered PCA where shape is het status with labels
tab_annot %>%
  ggplot(aes(EV1_filter, EV2_filter, color = wg_norm_depth)) +
  geom_point(aes(shape = het_status), size = 3,) +
  geom_label_repel(aes(label = acronym),
                   size = 3,
                  box.padding   = 0.5,
                  point.padding = 0.5,
                  max.overlaps = 50, 
                  nudge_x = 0.001,
                  segment.color = 'grey50') +
  scale_color_viridis_c(option = "magma") +
  theme_cowplot(20) +
  panel_border(color="black", size=0.75) +
  xlab(PC1_lab_filter) +
  ylab(PC2_lab_filter)
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_label_repel()`).
## Warning: ggrepel: 108 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Make plot of filtered PCA where shape is marine or freshwater
tab_annot %>%
  ggplot(aes(EV1_filter, EV2_filter, color = wg_norm_depth)) +
  geom_point(aes(shape = ecotype), size = 3,) +
  scale_color_viridis_c(option = "magma") +
  theme_cowplot(8) +
  panel_border(color="black", size=0.75) +
  xlab(PC1_lab_filter) +
  ylab(PC2_lab_filter)
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_point()`).

# Make plot of filtered PCA where shape is marine or freshwater with labels
tab_annot %>%
  ggplot(aes(EV1_filter, EV2_filter, color = wg_norm_depth)) +
  geom_point(aes(shape = ecotype), size = 3,) +
  scale_color_viridis_c(option = "magma") +
    theme_cowplot(20) +
  panel_border(color="black", size=0.75) +
  geom_label_repel(aes(label = acronym),
                   size = 3,
                  box.padding   = 0.5,
                  point.padding = 0.5,
                  max.overlaps = 50, 
                  nudge_x = 0.001,
                  segment.color = 'grey50') +
  xlab(PC1_lab_filter) +
  ylab(PC2_lab_filter)
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_label_repel()`).
## Warning: ggrepel: 108 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Plot relationship between EV1 and read depth
tab_annot %>%
  ggplot(aes(-EV1_filter, wg_norm_depth, color=ecotype, shape=het_status)) +
  geom_hline(data = sim_average, aes(yintercept = wg_norm_depth), linetype = "dashed", color = "grey", linewidth=0.25) +
  geom_point(alpha=0.5, size=3) +
  scale_color_manual(values=c("#d73027","#0072b2")) +
    geom_label_repel(aes(label = acronym),
                   size = 3,
                  box.padding   = 0.5,
                  point.padding = 0.5,
                  max.overlaps = 20, 
                  nudge_x = 0.001,
                  segment.color = 'grey50') +
      theme_cowplot(20) +
  panel_border(color="black", size=0.75) +
    xlab(paste("-",PC1_lab_filter, sep="")) +
  ylab("MYH3C3 normalized depth")
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_label_repel()`).
## Warning: ggrepel: 96 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Plot relationship between EV1 and heterozygosity
tab_annot %>%
  ggplot(aes(-EV1_filter, prop_het, color=ecotype, shape=het_status)) +
  geom_point(alpha=0.5, size=3) +
  scale_color_manual(values=c("#d73027","#0072b2")) +
    geom_label_repel(aes(label = acronym),
                   size = 3,
                  box.padding   = 0.5,
                  point.padding = 0.5,
                  max.overlaps = 20, 
                  nudge_x = 0.001,
                  segment.color = 'grey50') +
      theme_cowplot(20) +
  panel_border(color="black", size=0.75) +
    xlab(paste("-",PC1_lab_filter, sep="")) +
  ylab("Proportion heterozygous sites")
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_label_repel()`).
## Warning: ggrepel: 119 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Plot relationship between EV1 and F (inbreeding coefficient)
tab_annot %>%
  ggplot(aes(-EV1_filter, F, color=ecotype, shape=het_status)) +
  geom_point(alpha=0.5, size=3) +
  scale_color_manual(values=c("#d73027","#0072b2")) +
    geom_label_repel(aes(label = acronym),
                   size = 3,
                  box.padding   = 0.5,
                  point.padding = 0.5,
                  max.overlaps = 20, 
                  nudge_x = 0.001,
                  segment.color = 'grey50') +
      theme_cowplot(20) +
  panel_border(color="black", size=0.75) +
    xlab(paste("-",PC1_lab_filter, sep="")) +
  ylab("F (Inbreeding)")
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 29 rows containing missing values or values outside the scale range
## (`geom_label_repel()`).
## Warning: ggrepel: 119 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Get list of candidate California homoyzgotes
tab_annot %>% 
  filter(EV2_filter < -0.025, het_status == "likely-hom")
##             sample.id           EV1        EV2        EV3         EV4
## 1   BIGR_1_32_2007#03  0.0100751593 0.11578563 0.01831565 -0.10427624
## 2  BIGR_52_54_2008#02  0.0091435651 0.14479520 0.02631595  0.24085546
## 3   BIGR|1_32|2007#01  0.0188560556 0.16358342 0.02788093 -0.07274894
## 4   BIGR|3_63|2007#14  0.0162503009 0.16443493 0.03441498  0.01335552
## 5  BIGR|52_54|2007#04  0.0199480738 0.20172835 0.03309421  0.37149940
## 6  BIGR|52_54|2007#05  0.0168073085 0.19977535 0.03250645  0.34986706
## 7  BIGR|52_54|2007#12  0.0204752622 0.18804374 0.03377389  0.18704503
## 8  BIGR|52_54|2007#17  0.0193218937 0.20385198 0.03233429  0.37091308
## 9         CERC|X|X#04  0.0150473718 0.18145013 0.02665453 -0.16195633
## 10      ERBC|X|X#8770  0.0218436125 0.19946133 0.02331171 -0.20130306
## 11    FRIC_X_2003#C10  0.0210042351 0.18692614 0.03330537 -0.23635681
## 12        FRIL|X|X#05  0.0220998474 0.19757231 0.03149441 -0.24620270
## 13       GARC|X|X#711  0.0171456832 0.19325512 0.02681144 -0.18328100
## 14     LSOL|X|2012#04  0.0179523696 0.18814068 0.02989656 -0.09516079
## 15     OLNY_X_2007#03  0.0061191064 0.08980188 0.02003394 -0.10176181
## 16        PINC|X|X#03  0.0165511404 0.18198584 0.02801136 -0.17855641
## 17   SACK|X|2010#0898  0.0173504106 0.17199851 0.02840399  0.22559109
## 18        SALS|X|X#01  0.0181552697 0.18102229 0.02828708 -0.06651498
## 19        SAPC|X|X#01  0.0196026242 0.18944466 0.03052582 -0.19929522
## 20    SCRM|X|2010#873  0.0161646657 0.17495012 0.03989625  0.07423526
## 21   SCRS|X|2009#8253  0.0176966730 0.19152732 0.04437520  0.10215907
## 22   SJCR|X|2009#8212  0.0181230015 0.16922501 0.03711147  0.04985315
## 23   SLMW|X|2001#0918  0.0142021341 0.17006157 0.03816982  0.07694062
## 24     SSMC|X|2010#01  0.0171410153 0.17834774 0.03023856 -0.16256980
## 25        SUNC|X|X#04  0.0174810880 0.18174345 0.02659797 -0.19299190
## 26   WMSO_X_2002#bigf -0.0007224793 0.07434659 0.02166504  0.04705335
##                  samp   desc                 region    chr startpos  endpos
## 1   BIGR_1_32_2007_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 2  BIGR_52_54_2008_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 3   BIGR_1_32_2007_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 4   BIGR_3_63_2007_14 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 5  BIGR_52_54_2007_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 6  BIGR_52_54_2007_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 7  BIGR_52_54_2007_12 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 8  BIGR_52_54_2007_17 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 9         CERC_X_X_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 10      ERBC_X_X_8770 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 11    FRIC_X_2003_C10 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 12        FRIL_X_X_05 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 13       GARC_X_X_711 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 14     LSOL_X_2012_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 15     OLNY_X_2007_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 16        PINC_X_X_03 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 17   SACK_X_2010_0898 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 18        SALS_X_X_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 19        SAPC_X_X_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 20    SCRM_X_2010_873 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 21   SCRS_X_2009_8253 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 22   SJCR_X_2009_8212 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 23   SLMW_X_2001_0918 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 24     SSMC_X_2010_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 25        SUNC_X_X_04 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 26   WMSO_X_2002_bigf MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
##    numreads covbases coverage meandepth meanbaseq meanmapq acronym type
## 1       553     7912  73.7647   3.64833      21.6     46.7    BIGR real
## 2       971     8886  82.8454   6.50951      21.4     45.9    BIGR real
## 3      1032     8865  82.6496   7.12400      27.0     49.7    BIGR real
## 4      1634     9201  85.7822  11.25380      26.9     50.7    BIGR real
## 5      1057     8997  83.8803   7.21108      26.1     49.2    BIGR real
## 6      1222     9065  84.5143   8.39120      26.2     50.3    BIGR real
## 7      1445     8993  83.8430   9.99291      26.9     49.1    BIGR real
## 8      1019     8866  82.6590   6.96970      26.7     50.8    BIGR real
## 9      1301     9011  84.0108   8.97017      26.2     49.7    CERC real
## 10     1293     8508  79.3213   8.87749      26.2     50.8    ERBC real
## 11     1950     9238  86.1272  13.45810      21.9     49.1    FRIC real
## 12     1259     8728  81.3724   8.61001      24.9     51.1    FRIL real
## 13     1318     8707  81.1766   9.04326      26.1     49.9    GARC real
## 14     1107     9052  84.3931   7.56610      24.9     49.8    LSOL real
## 15      462     7475  69.6905   3.05146      20.4     47.1    OLNY real
## 16     1122     8821  82.2394   7.73690      26.3     50.8    PINC real
## 17     1452     8871  82.7056   9.95338      26.1     50.5    SACK real
## 18     1765     8993  83.8430  12.14660      25.8     50.9    SALS real
## 19     1087     8903  83.0039   7.46439      26.1     50.3    SAPC real
## 20     1269     8830  82.3233   8.72142      26.4     50.5    SCRM real
## 21     1392     8753  81.6054   9.64059      26.6     50.7    SCRS real
## 22     1177     9260  86.3323   8.14768      26.6     49.0    SJCR real
## 23     1252     8415  78.4542   8.58848      23.9     52.1    SLMW real
## 24     1467     9016  84.0574   9.99030      25.4     50.2    SSMC real
## 25     1206     9086  84.7101   8.25853      26.0     50.8    SUNC real
## 26      441     7512  70.0354   2.93735      22.2     45.0    WMSO real
##    weighted_mean_depth                                  pop coord_approx
## 1             7.478171                        Big River, CA         <NA>
## 2             7.524425                        Big River, CA         <NA>
## 3             5.188078                        Big River, CA         <NA>
## 4             5.252176                        Big River, CA         <NA>
## 5             5.034470                        Big River, CA         <NA>
## 6             5.888779                        Big River, CA         <NA>
## 7             5.732498                        Big River, CA         <NA>
## 8             4.859141                        Big River, CA         <NA>
## 9             5.619699   Cerrito Creek, Northern California         <NA>
## 10            6.101296              El Rosario Boca, Mexico            Y
## 11            9.623590                         Friant River         <NA>
## 12            5.989229                         Friant River         <NA>
## 13            5.887613   Garrity Creek, Northern California         <NA>
## 14            6.703666                      Lake Solano, CA         <NA>
## 15            8.340684              Olney Creek, California         <NA>
## 16            5.038420    Pinole Creek, Northern California         <NA>
## 17            5.840406          San Antonio Creek, VAFB, CA         <NA>
## 18            6.643173                    Salinas River, CA         <NA>
## 19            4.959425 San Pablo Creek, Northern California         <NA>
## 20            6.017638      Santa Clara River mouth, LA, CA         <NA>
## 21            6.563724            Santa Clara River, LA, CA            Y
## 22            5.821765 San Jacinto River, San Bernadino, CA            Y
## 23            5.752081  Sugarloaf Meadow, San Bernadino, CA            Y
## 24            6.874873                 San Simeon Creek, CA            Y
## 25            5.200986    Suisun Creek, Northern California            Y
## 26            7.117236           Williamsoni, CA; no plates         <NA>
##    GPS_north GPS_east mar_fresh             notes water_type
## 1     39.289 -123.747         M              <NA>     Marine
## 2     39.317 -123.686         F              <NA>      River
## 3     39.289 -123.747         M              <NA>     Marine
## 4     39.289 -123.747         M              <NA>     Marine
## 5     39.317 -123.686         F              <NA>      River
## 6     39.317 -123.686         F              <NA>      River
## 7     39.317 -123.686         F              <NA>      River
## 8     39.317 -123.686         F              <NA>      River
## 9     37.901 -122.281         F              <NA> Freshwater
## 10    30.036 -115.774         F              <NA>       <NA>
## 11    36.980 -119.731         F Completely plated      River
## 12    36.980 -119.731         F        Low plated      River
## 13    38.001 -122.322         F              <NA>      Creek
## 14    38.495 -122.033         F              <NA>       Lake
## 15    40.528 -122.384         F              <NA>      River
## 16    37.963 -122.202         F              <NA>      Creek
## 17    34.783 -120.536         F              <NA>      River
## 18    36.647 -121.702         F              <NA>      River
## 19    37.966 -122.320         F              <NA>      Creek
## 20    34.236 -119.257         M              <NA>     Marine
## 21    34.436 -118.612         F              <NA>      Fresh
## 22    33.765 -117.208         F              <NA>      River
## 23    34.179 -116.830         F              <NA>      Fresh
## 24    35.608 -121.091         F              <NA>      River
## 25    38.225 -122.107         F              <NA>      Creek
## 26    34.435 -118.198         F              <NA>      Fresh
##    PNW_independent_MvsF_c150 NorthEurope_independent_MvsF_c151
## 1                         NA                                NA
## 2                         NA                                NA
## 3                         NA                                NA
## 4                         NA                                NA
## 5                         NA                                NA
## 6                         NA                                NA
## 7                         NA                                NA
## 8                         NA                                NA
## 9                         NA                                NA
## 10                        NA                                NA
## 11                        NA                                NA
## 12                        NA                                NA
## 13                        NA                                NA
## 14                        NA                                NA
## 15                        NA                                NA
## 16                        NA                                NA
## 17                        NA                                NA
## 18                        NA                                NA
## 19                        NA                                NA
## 20                        NA                                NA
## 21                        NA                                NA
## 22                        NA                                NA
## 23                        NA                                NA
## 24                        NA                                NA
## 25                        NA                                NA
## 26                        NA                                NA
##    CaliforniaFreshwater_vs_AllPacificMarine_c153 c154_globalsuperglacial_FvsM
## 1                                              1                           NA
## 2                                              0                           NA
## 3                                             NA                           NA
## 4                                             NA                           NA
## 5                                             NA                           NA
## 6                                             NA                           NA
## 7                                             NA                           NA
## 8                                             NA                           NA
## 9                                              0                           NA
## 10                                             0                           NA
## 11                                            NA                           NA
## 12                                             0                           NA
## 13                                             0                           NA
## 14                                             0                           NA
## 15                                             0                           NA
## 16                                             0                           NA
## 17                                             0                           NA
## 18                                             0                           NA
## 19                                             0                           NA
## 20                                             1                           NA
## 21                                             0                           NA
## 22                                             0                           NA
## 23                                             0                           NA
## 24                                             0                            0
## 25                                             0                           NA
## 26                                             0                           NA
##    c155_global_FvsM used_joint_genotyping used _river_comparisons
## 1                 1                   Yes                     Yes
## 2                 0                   Yes                     Yes
## 3                NA                   Yes                     Yes
## 4                NA                   Yes                     Yes
## 5                NA                   Yes                     Yes
## 6                NA                   Yes                     Yes
## 7                NA                   Yes                     Yes
## 8                NA                   Yes                     Yes
## 9                 0                   Yes                    <NA>
## 10                0                   Yes                    <NA>
## 11               NA                   Yes                    <NA>
## 12                0                   Yes                    <NA>
## 13                0                   Yes                    <NA>
## 14                0                   Yes                    <NA>
## 15                0                   Yes                    <NA>
## 16                0                   Yes                    <NA>
## 17                0                   Yes                    <NA>
## 18                0                   Yes                    <NA>
## 19                0                   Yes                    <NA>
## 20                1                   Yes                    <NA>
## 21                0                   Yes                    <NA>
## 22                0                   Yes                    <NA>
## 23                0                   Yes                    <NA>
## 24                0                   Yes                    <NA>
## 25                0                   Yes                    <NA>
## 26                0                   Yes                    <NA>
##    used_pilot_analysis wg_norm_depth    ecotype    sex samp_length O(HOM)
## 1                 <NA>     0.4878640     Marine female          17   2830
## 2                 <NA>     0.8651173 Freshwater female          18   2984
## 3                 <NA>     1.3731481     Marine female          17   3307
## 4                 <NA>     2.1426930     Marine female          17   3382
## 5                 <NA>     1.4323414 Freshwater female          18   3438
## 6                 <NA>     1.4249474 Freshwater female          18   3466
## 7                 <NA>     1.7432035 Freshwater female          18   3300
## 8                 <NA>     1.4343480 Freshwater female          18   3414
## 9                 <NA>     1.5962013 Freshwater female          11   3377
## 10                <NA>     1.4550171 Freshwater female          13   3548
## 11                <NA>     1.3984490 Freshwater female          15   3477
## 12                <NA>     1.4375823 Freshwater female          11   3537
## 13                <NA>     1.5359807 Freshwater female          12   3439
## 14                <NA>     1.1286510 Freshwater female          14   3336
## 15                <NA>     0.3658525 Freshwater female          14   2349
## 16                <NA>     1.5355805 Freshwater female          11   3410
## 17                <NA>     1.7042274 Freshwater female          16   3465
## 18                <NA>     1.8284334 Freshwater female          11   3364
## 19                <NA>     1.5050920 Freshwater female          11   3463
## 20                <NA>     1.4493094     Marine female          15   3360
## 21                <NA>     1.4687684 Freshwater female          16   3519
## 22                <NA>     1.3995207 Freshwater female          16   3377
## 23                <NA>     1.4931082 Freshwater female          16   3399
## 24                <NA>     1.4531613 Freshwater female          14   3335
## 25                <NA>     1.5878779 Freshwater female          11   3390
## 26                <NA>     0.4127094 Freshwater female          16   2122
##    E(HOM) N_SITES       F  prop_hom    prop_het het_status   EV1_filter
## 1  2393.5    2911 0.84347 0.9721745 0.027825490 likely-hom  0.009546813
## 2  2493.0    3040 0.89762 0.9815789 0.018421053 likely-hom  0.008558535
## 3  2870.1    3509 0.68381 0.9424337 0.057566258 likely-hom  0.018374936
## 4  2882.7    3518 0.78594 0.9613417 0.038658329 likely-hom  0.015607905
## 5  2857.3    3497 0.90777 0.9831284 0.016871604 likely-hom  0.019485042
## 6  2919.5    3575 0.83372 0.9695105 0.030489510 likely-hom  0.016246984
## 7  2906.7    3561 0.60110 0.9267060 0.073294019 likely-hom  0.019994415
## 8  2832.0    3466 0.91798 0.9849971 0.015002885 likely-hom  0.018840145
## 9  2953.4    3609 0.64613 0.9357163 0.064283735 likely-hom  0.014492910
## 10 2954.2    3611 0.90408 0.9825533 0.017446691 likely-hom  0.021448016
## 11 2892.1    3537 0.90696 0.9830365 0.016963528 likely-hom  0.020476656
## 12 2950.9    3608 0.89194 0.9803215 0.019678492 likely-hom  0.021586141
## 13 2921.1    3570 0.79812 0.9633053 0.036694678 likely-hom  0.016493543
## 14 2957.8    3620 0.57111 0.9215470 0.078453039 likely-hom  0.017424375
## 15 1969.8    2372 0.94282 0.9903035 0.009696459 likely-hom  0.005606697
## 16 2877.2    3519 0.83017 0.9690253 0.030974709 likely-hom  0.015893340
## 17 2896.1    3541 0.88215 0.9785371 0.021462864 likely-hom  0.016888114
## 18 2992.8    3656 0.55968 0.9201313 0.079868709 likely-hom  0.017667124
## 19 2879.6    3519 0.91242 0.9840864 0.015913612 likely-hom  0.019073509
## 20 2905.6    3556 0.69863 0.9448819 0.055118110 likely-hom  0.015519429
## 21 2928.5    3589 0.89401 0.9804960 0.019504040 likely-hom  0.017058849
## 22 2916.7    3570 0.70457 0.9459384 0.054061625 likely-hom  0.017472125
## 23 2849.0    3479 0.87301 0.9770049 0.022995114 likely-hom  0.013551706
## 24 2885.8    3531 0.69622 0.9444916 0.055508355 likely-hom  0.016522975
## 25 2885.6    3524 0.79010 0.9619750 0.038024972 likely-hom  0.016938094
## 26 1764.2    2131 0.97547 0.9957766 0.004223369 likely-hom -0.001315031
##     EV2_filter  EV3_filter  EV4_filter
## 1  -0.11843145  0.10637948  0.06464475
## 2  -0.14876096 -0.24370123  0.17333823
## 3  -0.16703559  0.07210053 -0.07728973
## 4  -0.16835067 -0.01185221 -0.12689155
## 5  -0.20708829 -0.37565240  0.23755130
## 6  -0.20511225 -0.35305833  0.24246976
## 7  -0.19262885 -0.18516098  0.11130308
## 8  -0.20925397 -0.37454415  0.24857129
## 9  -0.18615652  0.16605975  0.04287893
## 10 -0.20445617  0.20657670  0.05838613
## 11 -0.19084870  0.23927903  0.13274268
## 12 -0.20173500  0.24919669  0.12662749
## 13 -0.19748182  0.18670337  0.09328415
## 14 -0.19260255  0.09769245 -0.01570642
## 15 -0.09186589  0.10387434  0.07147890
## 16 -0.18602453  0.18282818  0.09708258
## 17 -0.17701377 -0.23516977 -0.09265259
## 18 -0.18517259  0.06488567 -0.07658309
## 19 -0.19359763  0.20325700  0.12469692
## 20 -0.17863637 -0.07839920 -0.38149787
## 21 -0.19580976 -0.10793180 -0.48334857
## 22 -0.17284261 -0.05296481 -0.24755345
## 23 -0.17433837 -0.08285338 -0.38907754
## 24 -0.18226047  0.16421650  0.03677027
## 25 -0.18593108  0.19739168  0.10676946
## 26 -0.07622227 -0.04882559 -0.21633645
# Get list of candidate California homoyzgotes that are the closest to the bay area
tab_annot %>% 
  filter(EV2_filter < -0.025, het_status == "likely-hom", GPS_north < 38.5, GPS_north>37)
##        sample.id        EV1       EV2        EV3         EV4           samp
## 1    CERC|X|X#04 0.01504737 0.1814501 0.02665453 -0.16195633    CERC_X_X_04
## 2   GARC|X|X#711 0.01714568 0.1932551 0.02681144 -0.18328100   GARC_X_X_711
## 3 LSOL|X|2012#04 0.01795237 0.1881407 0.02989656 -0.09516079 LSOL_X_2012_04
## 4    PINC|X|X#03 0.01655114 0.1819858 0.02801136 -0.17855641    PINC_X_X_03
## 5    SAPC|X|X#01 0.01960262 0.1894447 0.03052582 -0.19929522    SAPC_X_X_01
## 6    SUNC|X|X#04 0.01748109 0.1817435 0.02659797 -0.19299190    SUNC_X_X_04
##     desc                 region    chr startpos  endpos numreads covbases
## 1 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020     1301     9011
## 2 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020     1318     8707
## 3 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020     1107     9052
## 4 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020     1122     8821
## 5 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020     1087     8903
## 6 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020     1206     9086
##   coverage meandepth meanbaseq meanmapq acronym type weighted_mean_depth
## 1  84.0108   8.97017      26.2     49.7    CERC real            5.619699
## 2  81.1766   9.04326      26.1     49.9    GARC real            5.887613
## 3  84.3931   7.56610      24.9     49.8    LSOL real            6.703666
## 4  82.2394   7.73690      26.3     50.8    PINC real            5.038420
## 5  83.0039   7.46439      26.1     50.3    SAPC real            4.959425
## 6  84.7101   8.25853      26.0     50.8    SUNC real            5.200986
##                                    pop coord_approx GPS_north GPS_east
## 1   Cerrito Creek, Northern California         <NA>    37.901 -122.281
## 2   Garrity Creek, Northern California         <NA>    38.001 -122.322
## 3                      Lake Solano, CA         <NA>    38.495 -122.033
## 4    Pinole Creek, Northern California         <NA>    37.963 -122.202
## 5 San Pablo Creek, Northern California         <NA>    37.966 -122.320
## 6    Suisun Creek, Northern California            Y    38.225 -122.107
##   mar_fresh notes water_type PNW_independent_MvsF_c150
## 1         F  <NA> Freshwater                        NA
## 2         F  <NA>      Creek                        NA
## 3         F  <NA>       Lake                        NA
## 4         F  <NA>      Creek                        NA
## 5         F  <NA>      Creek                        NA
## 6         F  <NA>      Creek                        NA
##   NorthEurope_independent_MvsF_c151
## 1                                NA
## 2                                NA
## 3                                NA
## 4                                NA
## 5                                NA
## 6                                NA
##   CaliforniaFreshwater_vs_AllPacificMarine_c153 c154_globalsuperglacial_FvsM
## 1                                             0                           NA
## 2                                             0                           NA
## 3                                             0                           NA
## 4                                             0                           NA
## 5                                             0                           NA
## 6                                             0                           NA
##   c155_global_FvsM used_joint_genotyping used _river_comparisons
## 1                0                   Yes                    <NA>
## 2                0                   Yes                    <NA>
## 3                0                   Yes                    <NA>
## 4                0                   Yes                    <NA>
## 5                0                   Yes                    <NA>
## 6                0                   Yes                    <NA>
##   used_pilot_analysis wg_norm_depth    ecotype    sex samp_length O(HOM) E(HOM)
## 1                <NA>      1.596201 Freshwater female          11   3377 2953.4
## 2                <NA>      1.535981 Freshwater female          12   3439 2921.1
## 3                <NA>      1.128651 Freshwater female          14   3336 2957.8
## 4                <NA>      1.535581 Freshwater female          11   3410 2877.2
## 5                <NA>      1.505092 Freshwater female          11   3463 2879.6
## 6                <NA>      1.587878 Freshwater female          11   3390 2885.6
##   N_SITES       F  prop_hom   prop_het het_status EV1_filter EV2_filter
## 1    3609 0.64613 0.9357163 0.06428374 likely-hom 0.01449291 -0.1861565
## 2    3570 0.79812 0.9633053 0.03669468 likely-hom 0.01649354 -0.1974818
## 3    3620 0.57111 0.9215470 0.07845304 likely-hom 0.01742438 -0.1926026
## 4    3519 0.83017 0.9690253 0.03097471 likely-hom 0.01589334 -0.1860245
## 5    3519 0.91242 0.9840864 0.01591361 likely-hom 0.01907351 -0.1935976
## 6    3524 0.79010 0.9619750 0.03802497 likely-hom 0.01693809 -0.1859311
##   EV3_filter  EV4_filter
## 1 0.16605975  0.04287893
## 2 0.18670337  0.09328415
## 3 0.09769245 -0.01570642
## 4 0.18282818  0.09708258
## 5 0.20325700  0.12469692
## 6 0.19739168  0.10676946
# Get list of candidate reciprocal deletion alleles (freshwater haplotype but 3 copy locus)
tab_annot %>% 
  filter(EV1_filter < -0.025, het_status == "likely-hom", wg_norm_depth < 1)
##             sample.id         EV1         EV2         EV3           EV4
## 1   COAT|X|2009#90234 -0.05449798 -0.02410928  0.01349470  0.0002058328
## 2      EDEN_X_2010#01 -0.05459037 -0.02388626  0.01330334  0.0009069261
## 3 LITC_23_32_2008#324 -0.05142116 -0.02235130  0.01390980  0.0010580689
## 4      QUIN_X_2003#02 -0.03965557 -0.01108763 -0.01249209 -0.0034433250
## 5      SDPY_X_2006#24 -0.05448931 -0.02413039  0.01289862  0.0012177776
##                  samp   desc                 region    chr startpos  endpos
## 1   COAT_X_2009_90234 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 2      EDEN_X_2010_01 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 3 LITC_23_32_2008_324 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 4      QUIN_X_2003_02 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
## 5      SDPY_X_2006_24 MYH3C3 chrXIX:2667295-2678020 chrXIX  2667295 2678020
##   numreads covbases coverage meandepth meanbaseq meanmapq acronym type
## 1      596     9189  85.6703   4.15234      27.6     51.7    COAT real
## 2      969     9320  86.8917   6.72665      24.0     50.7    EDEN real
## 3     1250     9496  88.5325   8.62987      22.0     50.3    LITC real
## 4      835     8873  82.7242   5.62698      20.2     51.6    QUIN real
## 5     1177     9471  88.2995   8.16530      22.5     52.0    SDPY real
##   weighted_mean_depth                           pop coord_approx GPS_north
## 1            5.146996      Coates Lake, Haida Gwaii         <NA>    53.669
## 2           11.307505        Eden Lake, Haida Gwaii         <NA>    53.845
## 3            8.777877      Little Campbell upstream         <NA>    49.012
## 4            6.702309           Quinalt, Washington         <NA>    47.471
## 5           11.755091 Serendipity Pond, Haida Gwaii         <NA>    54.028
##   GPS_east mar_fresh notes water_type PNW_independent_MvsF_c150
## 1 -132.880         F  <NA>      Fresh                         0
## 2 -132.746         F  <NA>       Lake                         0
## 3 -122.625         F  <NA>      River                        NA
## 4 -123.871         F  <NA>      Fresh                         0
## 5 -131.761         F  <NA>      Fresh                         0
##   NorthEurope_independent_MvsF_c151
## 1                                NA
## 2                                NA
## 3                                NA
## 4                                NA
## 5                                NA
##   CaliforniaFreshwater_vs_AllPacificMarine_c153 c154_globalsuperglacial_FvsM
## 1                                            NA                           NA
## 2                                            NA                           NA
## 3                                            NA                           NA
## 4                                            NA                            0
## 5                                            NA                           NA
##   c155_global_FvsM used_joint_genotyping used _river_comparisons
## 1               NA                   Yes                    <NA>
## 2               NA                   Yes                    <NA>
## 3               NA                   Yes                     Yes
## 4                0                   Yes                    <NA>
## 5               NA                   Yes                    <NA>
##   used_pilot_analysis wg_norm_depth    ecotype    sex samp_length O(HOM) E(HOM)
## 1                <NA>     0.8067502 Freshwater female          17   3820 3139.3
## 2                <NA>     0.5948837 Freshwater female          14   3836 3155.0
## 3                <NA>     0.9831386 Freshwater female          19   3670 3031.0
## 4                <NA>     0.8395585 Freshwater female          14   3242 2683.3
## 5                <NA>     0.6946182 Freshwater female          14   3836 3160.1
##   N_SITES       F  prop_hom    prop_het het_status  EV1_filter EV2_filter
## 1    3842 0.96869 0.9942738 0.005726184 likely-hom -0.05705539 0.02385962
## 2    3862 0.96322 0.9932677 0.006732263 likely-hom -0.05715463 0.02365214
## 3    3709 0.94248 0.9894850 0.010514964 likely-hom -0.05389208 0.02214684
## 4    3272 0.94904 0.9908313 0.009168704 likely-hom -0.04142741 0.01078058
## 5    3867 0.95615 0.9919834 0.008016550 likely-hom -0.05705723 0.02392578
##      EV3_filter    EV4_filter
## 1 -0.0006896213  0.0010690668
## 2 -0.0013086025  0.0012333431
## 3 -0.0013500294  0.0001571319
## 4  0.0050243160 -0.0130214279
## 5 -0.0015563032  0.0017423955